Pickup wiring diagrams

The car thinks the ignition is in the Start position, thus when you push the clutch in, it allows for the starter to be energized and engaged.

Something still is not wired correctly.
As a generality, it sounds like the momentary power wire (should only be hot when key is in Start position) is wired to the constant-supply power wire spot.

I found the info below, here - http://www.alarmsellout.com/support/diagrams/vehicle/HONDA%20ACCORD%201985-2005.pdf

12V CONSTANT WHITE or WHITE/BLACK
STARTER BLACK/WHITE
IGNITION BLACK/YELLOW
ACCESSORY YELLOW
SECOND ACCESSORY BLUE/WHITE

If you contact Alpine they will be able to tell you if there is an adapter that will plug right into your existing OEM harness. If not then, you'll have to figure out Which wires are which on your OEM harness, here is the Alpine wire code:
Alpine wiring help

HU harness color code pretty much universal.
red=ignition
yellow=battery +
black=ground
blue/white=remote turn on
blue=power antenna
pink/black=audio interupt in (not sure if you have one)
speaker wires
gray=right front
violet=right rear
green=left rear
white=right rear
speaker wire with black stripes is negative.

renunciation

to start with 12-3 wire is too small for a 50 amp load..but if you are doing 220 it goes like this you have a black ..white and green wire..black is hot..white is hot and green is ground ..if its 110..the black is hot.. white is ground and green is earth ground to casing metal..the bare copper wire is earth ground.. make sure no wires cross.. this will short it all out..

this might help
1994 Toyota Pickup Car Security Wiring Diagram
Battery Constant 12v+ Positive Wire (+): White And White/Red
Battery Constant 12v+ Positive Wire Location: Ignition Switch Harness
Starter Positive Wire (+): Black
Starter Positive Wire Location: Ignition Switch Harness
Ignition Positive Wire (+): Black/Yellow
Ignition Positive Wire Location: Ignition Switch Harness
Second Ignition Positive Wire (+): Black/Yellow Or Black/Red
Second Ignition Positive Wire Location: Ignition Switch Harness
Accessory Positive Wire (+): Blue/Red
Accessory Positive Wire Location: Ignition Switch Harness
Parking Light Negative Wire (-): Red/Black
Parking Light Negative Wire Location: At Steering Column Harness
Parking Light Positive Wire (+): Green
Parking Light Positive Wire Location: In Drivers Kick Panel
Power Door Lock Negative Wire (-): Blue/White
Power Door Lock Negative Wire Location: At Door Control Relay. The door control relay, is located behind the driver dash speaker.
Power Door Unlock Negative Wire (-): Blue/Yellow
Power Door Unlock Negative Wire Location: At Door Control Relay. The door control relay, is located behind the driver dash speaker.
Door Trigger Negative Wire (-): Black/White Or Black
Door Trigger Negative Wire Location: At 2-Pin Plug, Top Of Fusebox
Domelight Supervision Wire: Use Door Trigger, Requires Relay
Domelight Supervision Wire Location: N/A
Horn Negative Wire (-): Green/Red
Horn Negative Wire Location: At Steering Column Harness
Tachometer Wire Negative Wire (-): Black
Tachometer Wire Negative Wire Location: At Diagnostic Connector. The diagnostic connector, is located on the passenger inner fender near the fuse/relay box.
Brake Light Positive Wire (+): Green/White
Brake Light Positive Wire Location: At Switch Above Brake Pedal
Factory Alarm Disarm Wire (-): N/A
Factory Alarm Disarm Wire Location: N/A
Factory Anti-Theft System: N/A
Factory Anti-Theft System Location: N/A

if its a white wire,it goes into the bottom of the fuse block,which will have a black cover and green diagram.the big black fuse on the right will require a screwdriver to pop the clip,and it pushes down.you'll see after that.hope this helps,wes

the color of the plastic plug does not matter... You will have two injector plugs with white/red and yellow wires - those two go to cyl#'s 1 and 3.
the other two plugs will have white and blur wires.. those two plugs go to injectors # 2 and 4.