Where is the car located now? I'm busy this week and out of town for the weekend but should have some time early next week if you needed a second set of eyes on it...
It's in Newfield NY Place called Sureshift
I've experienced a couple no-start issues over the years but never one quite like you have. I've seen the big 3 plugs on the rear VC like Joe suggested cause a no-start condition. I've seen a bad set of injectors cause it (although they were out of a junkyard motor so unknown condition to begin with) and I've seen PATS issues. Given that your 95 has a potential wiring harness issue, that might be a good place to start looking.
yeah the wiring is pretty bad and I told them that, but the car was running when I took it there and they didn't decline to do the work so in my mind they should get it running. No?
When the shop did the transmission, did they pull the drivetrain out the top or did they use one of those splitters to push it apart enough to do the clutch (not sure this is feasible on a Contour but I've heard of it being done)? My suspicion is in the process of replacing the fan wiring harness they had some insulation flake off and cause a short. I'd check all the under-hood fuses for blown ones as that might point you in the right direction.
Not sure if they took it from the bottom or top? but yeah right after they changed the cooling fan harness it developed the no start.
What exactly does the car do now? I assume it turns over but does not fire? Does the fuel pump prime when you turn the key to run? Do you have spark? Does it cough at all when you try to start or just turn over?
As far as I know it does turn over .they can jump the fuel pump ,but it doesn't come on on it's own. and doesn't fire no spark.
EDIT: You could also buy my SVT before I opt to replace the rear subframe and keep it another year or two...