If you go with an aftermarket harness, it should be pretty much plug and play. The TBI's have been around for so long, and used so much (especially with the offroad crowd) that the harnesses are fairly reasonable. Since you are in need of an ECM, I would recommend the better '94-'95 ECM. I don't know for sure if it can be used with the 700R4, but I would check into it. Here is one other source for a harness.
http://www.fuelinjectionconnection.com/gpage.html
On those brakes, I don't really see anything wrong with the assembly.