Chrysler Repair: electical problems, 1997 plymouth breeze, plymouth breeze

Question
Im working on a 1997 plymouth breeze, this car came factory with manual windows and seats.
Just recently the interior wiring harness and interior was swaped , and now has 1997 chrystler cirrus interior with power windows and seats using the cirrus wiring harness(the engine harness was not touched),and all the electrical was working just fine, runs and drives well, up untill  a few week after the swap...what has happend is the factory anti theft system in the cirrus wiring harness has armed itself and I have no way of shutting it off, ive already have tried to replace the factory fuse tray back to stock but the system has the car in shut down mode, ive even tried using the key to look and unlook the front doors and in the ignition to reset the system but nothing shuts it off.
the car will start for about 3 sec. and shuts off every time , ...you can hear the alarm going off thru the horn and head light relays.
   Is there an over ride or something.
  Any info you can give would be much appriciated

                      Thank You

Answer
Hi Toby,
I have not actually worked on the vehicle theft security system, only read about it in various manuals that I have. In theory if the system were working properly the engine defeat mode would be cancelled out by doing the key lock/unlock that you say you have done. I suspect that this happened because of the swap, though I am not clear whether the car had this VTSS system originally or did you modify it or merely add it during the swap? In a newly installed system at the factory the VTSS doesn't actually begin to work until 20 key on-off cylcles. So maybe that is why you had no problem until few weeks after the swap.
In any case I would wonder if you changed out the body computer in the swap and that might have been the reason for the snafu. The other possibility is that the door switch wiring was not installed properly or disturbed in the swap. I have the '96 Cirrus/Status shop manual and wiring diagram including 3 pages that show the VTSS. It is mentioned there that with a diagnostic readout box you can do a self-diagnostic test of each of the systems components to try and isolate one that is not being seen by the body computer which may help you solve the issue. But I suspect that a DRB and a Body Diagnostic manual (which I don't have) for '97 may be necessary to reverse the situation. That may mean towing the car to a dealer who is knowledgeable and equipped to test the system with the DRB and diagnose what is the reason for the persistant shutdown/inability to disarm the system. So tell me about the VTSS history on the vehicle (did it have it before the swap, did you change it in anyway during the swap, if so...).
I can xerox and snail mail you the VTSS pages from the '96 manual. So give me a postal address if you want those.
Roland