Questions swapping 96 GTS to PW/PDL

I’ve swapped a 96 Mustang GTS to power windows and power door locks using parts and harnesses from a 98 Mustang V6 with remote keyless entry. Besides the obvious hardware and harness swaps in the doors, there was an additional harness that needed to be changed. This harness plugs into the interior fuse panel bulkhead connector as well as the under hood fuse panel through a bulkhead connector in the firewall. It also feeds the wiper motor, master cylinder, power windows and door locks, speakers throughout, power mirrors, clutch safety, stoplight switch, power seats, taillights, fuel cutoff, fuel level indicator, and fuel pump and numerous other things that I’ve since forgotten.

The car would not start, the dome light did not work, the left side turns signal blinked quickly and the left front bulb did not illuminate. The left front bulb did not illuminate when the headlights were on either. As well, the air bag indicator came on intermittently. I quickly discovered that the constant +12V was missing at the ignition switch. After looking over the bulkhead connector in the firewall, I noticed a lot of different color codes of wires in locations when compared to the original harness bulkhead. I noticed that for some unknown reason, the wires in position 2 and position 22 were swapped in the 98 harness. I swapped them and immediately I could start the car.

Since then, I have gone through every position of both bulkhead connectors and written the color codes of each position for the original 96 harness and the current 98 harness. There are still about 10 positions out of 24 that have different color wires in them. 5 of the 10 could possibly be moved to match, but the other 5 are not the same. I also don’t know if I should just swap them because I don’t want to cause a meltdown.

Thing is that the schematics (Mitchell and Haynes) for the 96 and 98 show that all except like 2 wires should have the same color code. I don’t know if that means the schematics are wrong, or if the car is actually a late model 95 instead of a 96, or maybe both.

Does anyone out there have access to Ford schematics for a 95, 96, and 98? If so, can you get copies covering these items for me?

I’m also sure that someone out there has already done this. If so, can you please fill me in with the details?

Thanks in advance for any help you can provide.
 
Since you are swapping in the remote entry stuff, isn't that still located in the trunk? It, along with the factory alarm box, were tucked away behind the panel on the driver's side of the trunk on my '95.

I know that with my remote entry system, and factory alarm, there was a connector which allowed/disallowed the factory alarm to disable the starter. You either jumpered it, or not. Since you mentioned you can't start your car, it got me to thinking of this.