Turns out the wiring harness I have on hand is a 99 Auto harness. The car will not start with that combo, right? Am I screwed into buying another one or can something be done to make the harness work like a simple 95 would?

Not sure exactly on the specifics of the 99 harness, but it's auto and Fed spec (Canada).
The 95 ECU has a manifacturing date of 12/94 and is from an SE 5-speed.

 

Not sure. I think the main concern is that the 99's have the immobilizer if i am correct. I think that is the only difference. In addition, the guage cluster from the 99 has digital reading for miles unlike the 95-98. Someone else jump in.

 

One of hte crank wires is in a differ location. As are some O2 sensor wires(rear o2). Fuel pump relay CEL will come up.

 

Check the wiring diagram. I know JWT got it to work by just swapping a few wires. You will definitely have extra connections though.