98 mustang anti theft system not working correctly.

The electronic door lock control system consists of the remote anti-theft personality (RAP) module, and two three-button transmitters. The RAP module controls the door locks through the use of external relays located in the relay box, on the LH side of the lower instrument panel. The RAP module also controls the anti-theft system.
Keyless entry remote transmitters are programmable. All transmitters for the vehicle must be set at the same time. When troubleshooting the system, both transmitters are needed to perform the pinpoint tests.
To unlock the driver door and disarm the anti-theft system, press the unlock button on the keyless entry remote transmitter one time. To unlock both doors, press the unlock button a second time within five seconds.
To lock all doors and arm the anti-theft system, press the lock button on the keyless entry remote transmitter one time. To confirm that the doors have locked and the anti-theft system has armed, press the lock button a second time within five seconds. The horn will chirp once to notify that all doors are closed and locked and the alarm is armed. The horn will chirp twice if any door is still ajar.
NOTE: The remote entry features will not function when the key is in the RUN or ACC position.
To activate the panic alarm, press the red panic button on either transmitter. The horn will sound and the parking lamps will flash for a maximum of three minutes.
To deactivate the panic alarm, press the red panic button again or turn the ignition to the ON position.


Inspection and Verification

1. Verify the customer concern by operating the electronic door lock control system.

1. Visually inspect the following for obvious signs of mechanical and electrical damage:
   
   Visual Inspection Chart Mechanical Electrical
   • Binding latches
   • Fuse(s)
   • Relays
   • Wiring harness
   • Loose or corroded connections
   • Remote anti-theft personality (RAP) module
   • Remote entry transmitter
   • Door open warning lamp switch

1. If the concern remains after the inspection connect the scan tool to the data link connector (DLC) located beneath the instrument panel and select the vehicle to be tested from the scan tool menu. If scan tool does not communicate with the vehicle:
   • check that the program card is properly installed.
   • check the connections to the vehicle.
   • check the ignition switch position.

1. If the scan tool still does not communicate with the vehicle, refer to the scan tool manual.

1. Perform the DATA LINK DIAGNOSTIC TEST. If the scan tool responds with:
   • CKT914, CKT915 or CKT70=ALL ECUS NO RESP/NOT EQUIP, refer to Section 418-00 .
   • NO RESP/NOT EQUIP for RAP, go to Pinpoint Test A.
   • SYSTEM PASSED, retrieve and record the continuous diagnostic trouble codes (DTCs), erase the continuous DTCs and perform self-test diagnostics for the RAP module.

1. If the DTCs retrieved are related to the concern, go to the RAP Module Diagnostic Trouble Code (DTC) Index.

1. If no DTCs related to the concern are retrieved, proceed to the Symptom Chart.

RAP Module Diagnostic Trouble Code (DTC) Index
RAP Module Diagnostic Trouble Code (DTC) Index DTC Description DTC Caused By Action B1309 Power Door Lock Circuit Short to Ground RAP GO to Pinpoint Test B . B1341 Power Door Unlock Circuit Short to Ground RAP GO to Pinpoint Test B . B1522 Hood Switch Circuit Short to Ground RAP REFER to Section 419-01 . B1562 Door Lock Cylinder Circuit Short to Ground RAP REFER to Section 419-01 . B2425 Keyless Entry Out of Synchronization RAP GO to Pinpoint Test B .

So if you are asking about disabling the anti-theft, you cannot as it was installed for a reason and it was not made to completely disable. However, there are several ways to reset the anti-theft: (1) push the panic button on your remote. (2) Ensure all of the doors, trunk and hood are closed and lock and unlock the doors.


More than likely, you will find that you have a problem with one of these switches or the wiring and I would put my money on the switch as they are known for going bad. Many times, you can simply push them in and out so that it breaks through the carbon buildup and makes contact but if the switch has failed, this will not work.


The 97 uses a 'normally open' (if I remember correctly) switch so you can bypass the switch by simply unplugging it. If it is a 'normally closed' switch (in case I don't remember correctly) you can put a jumper wire across the contacts to disable the switch.


If you need a recommendation for a repair shop, go see Jack Ellenburg at Jack's H&W Auto and Truck repair on Miles Road. He is by far the best Ford/Lincoln mechanic in town and the person may other shops take their vehicles to when they can't fix them. Including the dealers. :) And no, I do not work for him, just know of his work and reputation.

Ford sold a Ford branded alarm through the parts department. These sometimes were a dealer installed option on new cars. Mine would randomly stop responding to the remote and I would have the same symptoms as you describe. I had it removed and the original equipment factory system still worked. Be warned, if you have the Ford "accessory" alarm, your key fobs (remotes) are different and the method to program them is different from what you will read online. You can tell if you have the system by looking at your key fob. The standard Mustang key fob is a 4 button (lock, unlock, panic, and trunk). The accessory alarm uses a 3 button remote and clicking unlock twice would pop the trunk. I really wish I had a picture of the remote because there are 3 button Ford key fobs for cars without a trunk release although I don't think you should have one on a Mustang. Long story short, if you have the accessory alarm, you can solve your problem by having it removed but you will need new 4 button key fobs to remotely lock/unlock your doors

Does it open the trunk? Does the panic button work? More than likely, the batteries are too low and should be replaced.

anti theft light should blink every few seconds.

try disconnecting the battery for 15 minutes.

Anti-Theft-Perimeter The perimeter anti-theft system consists of the following components:

• anti-theft indicator (THEFT)
• remote anti-theft personality (RAP) module
• hood switch
• keyless entry remote transmitter
• deck lid ajar switch

NOTE: The remote entry features will not function when the ignition switch is in the RUN or ACC position.
Up to four keyless entry remote transmitters (15K601) can be programmed at one time.
The keyless entry remote transmitters :

• Are programmable.
• Must be set at the same time.
• House four buttons.
• House three buttons (Mexico Anti-Theft System only).

Programming
Refer to Section 501-14B.
Inputs and Outputs
The remote anti-theft personality (RAP) module receives input from the following components for anti-theft operation:

• Hood switch.
• Deck lid ajar switch.
• Keyless entry remote transmitter.
• Power door lock switches (LH and RH).
• Door courtesy input.

The RAP module distributes output to the following for the anti-theft system:

• Power door unlock relay.
• Power door lock relay.
• Liftgate unlock relay (Wagon)
• Park lamps relay.
• HORN relay.
• Dome lamp.
• THEFT indicator.
• Deck lid release.

Arming
The anti-theft system can be armed if:

• The ignition switch is in the OFF position.
• The panic alarm is off.
• All doors are closed.

NOTE: If a door is open, the anti-theft system is prearmed and waiting for all the doors to be closed. The THEFT indicator will remain illuminated for up to 30 minutes waiting for all the doors to be closed. If a door remains open after 30 minutes, the THEFT indicator will turn off and the system will return to a disarmed state. After all doors are closed and the 30 second prearm (continuous THEFT indicator illumination) is complete, the system is armed.
NOTE: If the theft LED does not flash after 30 seconds, check the LED FLASH PID to see if the feature is enabled.
The anti-theft system will be armed when the lock button on the keyless entry remote transmitter is pressed, all doors are closed and 30 seconds have elapsed.
When the system is armed, the THEFT indicator will flash quickly until the system is triggered or disarmed.
Disarming
NOTE: Using a key in a door lock cylinder to unlock is not a valid method of disarming the anti-theft system.
Untriggered System
NOTE: If the driver arms the system and remains in the vehicle, an untriggered system can be disarmed by turning the ignition switch to the ON position.
An untriggered alarm system can be disarmed by pressing the unlock button on the keyless entry remote transmitter.
Triggered System
NOTE: If the hood or trunk are open when the system is armed, it must be closed and opened again before it can trigger an alarm.
An armed anti-theft system can be triggered by the following conditions:
The deck lid door, liftgate, hood or any door is opened using a key, inside door handle, hood release, etc.

• The keyless entry remote transmitter can activate a panic alarm which is similar to the anti-theft alarm, but does not cause the THEFT indicator to flash.

A triggered alarm system can be disarmed by:

• Pressing the unlock or panic button on the keyless entry remote transmitter.
• Turning the ignition switch to the ON position.

Alarm State When Battery Power Is Cycled
When the RAP module is supplied power the first time at the vehicle assembly plant, the system will be in the disarmed state. The RAP module will remember whether it is armed, disarmed or triggered in its non-volatile memory. When the battery positive cable is removed and then reconnected, the system will return to the state it was in just before the battery was disconnected. If the system is in any prearm state, then the system will return to a disarmed state when the battery is disconnected and then reconnected.

This is from Ken on CarPros:
Here is the way to reset the security system.

https://www.2carpros.com/articles/how-to-reset-a-security-system

Here is the systems descriptions

There are 2 security system, namely anti-theft and immobilizer.

Here are the 2 systems.

DESCRIPTION & OPERATION
Anti-theft system is controlled by Body Control Module (BCM). BCM receives signals from hood switch, trunk switch, door switches and Local Control Modules (LCMs). There are 5 LCMs located throughout vehicle.

To set anti-theft system in armed mode, remove ignition key, close all doors, trunk and hood. Lock doors using key or remote controller. The SECURITY light will illuminate for 30 seconds, then flash in 2.4 second intervals, indicating system is in armed mode.

To cancel armed mode, unlock and open any door or trunk lid using key or remote controller. SECURITY light will flash every second, indicating system is disarmed.

Alarm will activate (horn sounds, headlights flash and starter circuit is disabled) if any of the following conditions occur while system is in armed mode:

Engine hood or trunk lid is opened using the hood or trunk lid release.
Door(s) is unlocked without key or remote controller.
Tampering with any door/trunk lid key cylinders.
To deactivate anti-theft system, unlock door or trunk using key or remote controller.

If it is the immobilizer that is preventing the engine from being started, ensure you have the correct key and the transponder is intact. Quite often keys are dropped and if it breaks open, the internals would scatter all over. When this occurs, there is a tendency for the transponder to be lost.

Please let us know happens so it will help others.

Best, Ken
I hope that helps you out!

your battery is probably to low to start the car

The ignition lock anti-theft switch (19A438) detects if the ignition key cylinder is broken or "slam pulled" during a theft. The ignition lock anti-theft switch is always monitored by the remote anti-theft personality (RAP) module. This allows the alarm system to be triggered in the case that the ignition lock anti-theft switch detects tampering of the ignition key cylinder (even in the event that the alarm is not active at the time).
Refer to the Section 501-14B for more details on the keyless entry remote transmitter (15K601).
The door open warning lamp switch (14018) communicates to the RAP module through the generic electronic module (GEM). This input to the RAP will cause the anti-theft alarm to be sounded if the anti-theft alarm was armed.
The door disarm switches are assembled into both LH and RH lock sets. The door disarm switch must be triggered before the mechanical lock unlocks. This is to prevent the anti-theft alarm from activating when it should have been disarmed.
The RAP module controls the anti-theft system and is the brains of the keyless entry system. The RAP module communicates with the GEM to request that the interior lights be turned ON/OFF with use of the keyless entry remote transmitter, and the GEM communicates to the RAP to inform when the door is opened. Refer to Section 418-00 for inter-module communication.
The RAP module has three wire connectors attached to it:

• The antenna for the keyless entry remote transmitter.
• 26 circuit connector (C256).
• 22 circuit connector (C257).

In addition to the perimeter alarm that uses the door open warning lamp switch, the RAP module also uses the ignition lock anti-theft switch and the autolock/relock feature to prevent theft of the vehicle. For a full description of the autolock/relock system, refer to Section 501-14B .
The THEFT LED is found on the instrument panel between the tachometer scale and the needle pivot point. The LED is illuminated during prearming and flashes when armed or triggered.
Prearming and Arming the System
The system can be armed if:

• The ignition is OFF.
• The PANIC alarm is OFF.
• All doors are closed.

There are two ways to prearm the system:

• Press the LOCK button on the transmitter.
• Open a door, press the power door lock button and close the door.

After 30 seconds the system will be armed and the theft indicator in the cluster will flash every two seconds.
Disarming an Untriggered System
An armed system will be disarmed with one of these valid actions:

1. Pressing the UNLOCK button on the transmitter.

1. Placing a key in the door and turning to UNLOCK.

1. Turning the key to RUN or ACC.

The anti-theft alarm can be triggered by the following conditions:

• The ignition cylinder is damaged with or without the RAP being armed.
• A door is opened without disarming the armed RAP module.

The remote transmitter can activate a panic alarm which is similar to an anti-theft alarm, but does not deactivate the starter or cause the theft indicator to flash.
Disarming a Triggered System
If the system has been triggered, (the horn honks, the lights flash, and an external starter interrupt relay is engaged), the system can be disarmed by:

1. Pressing the UNLOCK or PANIC button on the transmitter.

1. Putting a key in the door and unlocking the door.

1. Turning the ignition to RUN/ACC (Turning the key to RUN/ACC will not disarm an alarm that has been triggered by the ignition lock anti-theft switch.).

Section 13-11: Anti-Theft System, Active 1998 Windstar Workshop Manual DESCRIPTION AND OPERATION Anti-Theft Alarm System NOTE: The system immediately monitors the ignition key lock cylinder upon removal of the key from the ignition. It is not necessary to arm the system for ignition key lock monitoring.

The anti-theft alarm system:

• protects the vehicle from unauthorized entry into the passenger compartment, engine compartment and cargo area.
• monitors the status of the ignition key lock cylinder.
• is controlled by a remote anti-theft personality (RAP) module. The remote anti-theft personality module also controls the electronic door lock functions. Refer to Section 01-14B for more details.
• when armed, detects unauthorized entry into the passenger compartment by using an input from the GEM module regarding the state of the door or liftgate (open or closed).
• protects the engine compartment with a hood switch which is located on the LH cowl vent panel and is part of windshield wiper motor wiring (17A477) .
• triggers an alarm if the ignition lock cylinder is forcibly removed from the steering column.

Once triggered, the system responds by:

• flashing the low beam headlamps, the parklamps, rear lamps and the alarm indicator warning light emitting diode (LED).
• sounding the horn (13832).
• disabling the starter circuit until the system is disarmed.

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Remote Anti-Theft Personality Module

• The remote anti-theft personality module is located behind the instrument panel (04320).
• It contains a radio receiver that receives the RF signal from the keyless entry remote transmitter (15K601) through the alarm and lock system antenna (15603) and sends the appropriate command to the power door locks, the horn relay, or the generic electronic module.
• The remote anti-theft personality module is equipped with an internal backup power supply which holds the programmed code in memory in the event the vehicle battery is disconnected.

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Remote Anti-Theft Personality Module Removal

1. Disconnect battery ground cable (14301). Refer to Section 14-01 .
   

1. Remove radio. Refer to Section 15-01 .
   

1. Remove lower instrument panel center finish panel. Refer to Section 01-12 .
   

1. Lower glove box.
   

1. Remove two remote anti-theft personality module bracket retaining screws.
   

1. Disconnect electrical connectors and alarm and lock system antenna (15603).
   

1. Remove remote anti-theft personality module and bracket.
   

1. Remove remote anti-theft personality module from mounting bracket.
   

Installation

1. To install, follow removal procedure in reverse order.
   

1. Tighten remote anti-theft personality module bracket retaining screws to 6-8 Nm (54-70 lb-in).
   
   

Components The system is composed of the following components:

• remote anti-theft personality (RAP) module with integral antenna
• alarm indicator LED
• door lock cylinder switch RH, door lock cylinder switch LH
• liftgate door lock cylinder switch (220A40)
• hood switch (part of windshield wiper motor wiring (17A477))
• ignition lock anti-theft switch (19A438)

The following vehicle components are also used by the anti-theft alarm system:

• generic electronic module
• power door lock switch (14028)
• door open warning lamp switch (14018)
• autolamp relay (14N089)
• horn relay and bracket (13853) and horn (13832)
• low beam headlamps
• rear lamps (13404) and parking lamps (13200)
• starter relay
• door lock relays
• keyless entry remote transmitter (15K601)

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Disarming an Untriggered System NOTE: A perimeter alarm will "shut off" after 165 seconds, but the system is still triggered and is not disarmed.

An armed but untriggered perimeter anti-theft system can be disarmed by one of the following four events:

1. Unlock the doors by pressing the keyless entry remote transmitter (15K601) UNLOCK button once.
2. Unlock any door with a key.
3. Turn ignition switch to RUN or ACC.
4. The remote entry PANIC button will disarm the anti-theft system only when the perimeter alarm is triggered and sounding.

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System Triggering NOTE: Although the remote entry PANIC alarm is not associated with the monitoring of the vehicle, the user will frequently say that the theft system was triggered when actually the keyless entry remote transmitter PANIC button was inadvertently pressed. A panic alarm will not flash the THEFT indicator.

The alarm can be triggered by the following events if the system has been armed and has not been disarmed first:

• Open any door or liftgate.
• Open the hood (16612) (if the hood was open when the system was armed, it must be closed before it can trigger the alarm).
• Dislodge the ignition key lock cylinder.
• The anti-theft system may be triggered inadvertently when the module is disconnected and then reconnected. To avoid inadvertent alarm triggering, disconnect the smaller 22-way connector first.

When the system is triggered the perimeter alarm will operate as follows: The remote anti-theft personality module will pulse the following outputs at approximately 1.3 Hz, 50 percent duty cycle for two minutes 45 seconds for North America. NOTE: Other perimeter alarms can be programmed for the system.

• low beam headlamps
• parking lamps
• horn
• THEFT indicator

The perimeter alarm can be retriggered, after a perimeter alarm has sounded for 165 seconds. After a perimeter alarm has timed out, if any trigger input is first seen as normal and is then seen in its trigger state, the perimeter alarm will be retriggered. The perimeter alarm can be triggered a total of three times between an arming sequence and a disarm event. An active panic alarm will be deactivated when a perimeter alarm is triggered (a perimeter alarm overrides a panic alarm).

The chip is in the key. Either the key has lost it's program or the transceiver is not recognising the key. Try another key if you have one.