Your power transitor plugs are different. If you can get a 1991-94 ecu and 1991-94 tansitor and coil will make it easier. Also a less of a headache. You should check out
www.4g61t.com for info becasue they do 46g3t swaps in colts and give out a lot of info.
How did you get the power transitor plug to fit the 90 transitor?