Lock cylinder was ripped out.ive replaced cylinder and key.anti theft is still activated,and tower ford cant reprogram new lock codes because there computer does'nt register when plugged in to cpu.it turns over but wont start.how do i disable anti-theft altogether

Hello Cathy

It does indeed have keyless entry. It needs reprogramming when you get a new remote. Also if you disconnect the battery. Usually a local car alarm fitting shop, or an auto-electrician will do it. Plus of course a Ford dealership.

https://www.google.com/search?q=Keyless+Entry+Remote+System+1999+Ford+Windstar

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You can't just change parts an expect it to work , software , modules won't let it work . You have to take it to the dealer or have a mobile lock smith fix it , reprogram it ETC...
Anti-Theft -Passive Anti-Theft System (PATS) The passive anti-theft system (PATS) contains the following components:

• theft indicator
• encoded ignition key
• PATS transceiver module
• powertrain control module (PCM)
• standard corporate protocol (SCP) communication network
• Passive Anti-Theft System (PATS) -Diagnostic Trouble Codes (DTC) Index Powertrain Control Module Diagnostic Trouble Code (DTC) Index DTC Description Source Action B1213 Anti-Theft Number of Programmed Keys is Below Minimum PCM GO to Pinpoint Test F . B2431 Transponder Program Failure PCM VERIFY if using correct PATS key, if defective USE new key. B1342 ECU is Defective (EEFROM in PCM not working) PCM INSTALL a new PCM. REFER to Section 303-14 . B2103 Antenna Not Connected PCM GO to Pinpoint Test A . B1600 PATS Ignition Key Transponder Signal is Not Received PCM GO to Pinpoint Test B . B1601 PATS Received Incorrect Key-Code From Ignition Key Transponder PCM GO to Pinpoint Test C . B1602 PATS Received Invalid Format of Key-Code From Ignition Key Transponder PCM GO to Pinpoint Test D . B1681 PATS Transceiver Module Signal is Not Received PCM GO to Pinpoint Test E . - All Other DTCs PCM REFER to Section 419-10 .

have the key fob reprogrammed to the barrel

Chipped ignition ? Key's on your car do not have transponder chip . Replacing Keys
The ignition lock cylinder and keys do not contain any coded electronic components. The lock cylinder housing contains the coded electronic components. Changing an ignition lock cylinder or replacing a key is a purely mechanical process which does not affect the vehicle theft deterrent system. To replace an existing key, simply cut a new key to match the existing one. If no keys are available, the lock cylinder must be changed. To change the lock cylinder, simply replace the existing lock cylinder with one of the same type.

The reason your anti-theft is active is the new column has a different key than your original. The chip that is in the key is different than the one that is suppose to go to your vehicle. You need to order a new lock cylinder from your local GM dealer for your VIN number.

Ignition what ? Switch ,Ignition lock cylinder ? New keys ? do they have the transponder pellet in the head. Do you have a security lit flashing when trying to start the vehicle ?
SECTION 419-01: Anti-Theft - PATS 1999 Mustang Workshop Manual GENERAL PROCEDURES Procedure revision date: 11/06/1998 Key Programming -Erase All Key Codes and Program Two Keys
Special Tool(s) > New Generation STAR (NGS) Tester or equivalent
418-F048 (007-00500) NOTE: This procedure is used when a customer needs keys programmed into the system and does not have two programmed ignition keys available. This procedure is also useful when programmed ignition key(s) have been lost or the ignition switch assembly has been replaced, and it is desired to erase key(s) from the passive anti-theft system (PATS) memory.
NOTE: This procedure will erase all programmed ignition keys from the vehicle memory and the vehicle will not start until two keys have been reprogrammed to the vehicle.
NOTE: Two PATS encoded keys with the correct mechanical cut must be available to perform this procedure. One or both of them may be the customer's original keys.
NOTE: If additional keys are to be programmed, refer to Key Programming - Program a Key Using Two Programmed Keys. If the remaining keys are with the customer and are not available with the vehicle, then instruct the customer to refer to the Owners Guide under the "Programming Spare [SecuriLock ® (North America), Safeguard ® (U.K.) or PATS for all other markets] Keys Procedure" for instructions on programming the remaining keys.

1. Turn the ignition switch from OFF to RUN.

1. Enter New Generation STAR/Service Bay Diagnostic System (NGS/SBDS). Follow the SECURITY ACCESS PROCEDURE to obtain security access.

1. From NGS/SBDS menu, select IGNITION KEY CODE ERASE.

1. NOTE: Do NOT select any additional commands from this menu.
   Turn the ignition switch to OFF and disconnect NGS.

1. Insert the first encoded key into the ignition lock cylinder and turn the switch to RUN for three seconds.

1. Insert the second encoded key into the ignition lock cylinder and turn the switch to RUN for three seconds.

1. The vehicle should now start with both ignition keys.

You'll need to take to the dealer

If it is a different lock cylinder and key than the original, then you will need to use the original lock cylinder and keys. Or have the theft deterrent system reprogrammed to the existing keys that are in the steering column

The old key may have an induction chip in to deactivate the anti theft system. Does it have a red insert (chip) in the key handle? Get the old key and place it as close to the ignition barrel as possible. Seen this done on a number of occasions to save paying for a key reprogram.

Check out this link for useful info and some Do it Yourself options http://vatspasslockpasskeysecurityhelp.yolasite.com/

The sensor is part of the ignition key lock cylinder, so the part and labor will be around $200-$300 depends on your local labor rate, the dealer must do this repair because the new lock cylinder key code must be programmed into the VATS module.