In an earlier post, I stated that the cars were the same until (what) 2005.... I subsequently learned that in 1999, Ford re-skinned the car.... the basic chassis is supposedly virtually identical to the '94 to'98 cars and by virtue of that, the installation of a windsor engine should be able to be done with "factory" mount parts etc.....
Your question about the factor wiring harness now.... is that in regards to class legality or expediency? I have never to my recollection seen anything in the rules that states the original wiring haness must be used....but then, I have never dun production or gas coupe either.... it appears to me that how you get the mandatory equpment on the vehicle into operating condition is not the question .... the rules are that it must be operable and do not state by what wires or wiring harness(es) the electricity must flow....
My personal philosophy in matters like this is taken from racing legend Smokey Yunick who stated that, if the rules don't say you can't, then it's LEGAL!