ok i know there has been the 99 to 95 ecm swap, but was wondering if a 96 engine harness and ecu would be a direct swap into a 99...I have a 99 i30t w/ dek swap and now its 5spd swapped. Even though running the 99 ecu and swapping a few pins around is possible to run 95ecu and can i just swap everything (harness and ecu) without having to switch pin outs? reason i'm asking is i have the 96 harness i got w/ my 96 5 speed conversion stuff so all i need is the ecu which i can get for like $40 bucks. Any input is greatly appreciated, thanks
You'll run into problems with the egr for sure, and possibly evap. Not sure about evap, I know the '99 evap has additional equipment like the vacuum canister hidden behind the fender area. The egr on '99's is not a simple selenoid set-up, it has a 6 or 8 pin connector & circuit board right over the valve itself. You could always run the 95-98 style egr, but that install would be a nightmare because I am 50% sure (basically I'm not sure) that you would have to swap out the pipe on the rear header, and THAT thing is usually 100% impossible to do even out of the car in some situations. Code-wise you would have a basket case on your hands, running and driving you'd never know the difference though.
well if your referring to the black canister in the engine bay on the right front when your looking down at the motor....that is not connected to anything ever since the swap. Would it be worth swapping as far as a power diff? my buddies dek went 13.6 at 101....with the same mods except his is a 96 and he had a jwt ecu....i am running into an issue with the rpms though, sometimes if i punch it in whatever gear mainly 1st and 2nd it will hit a "fuel cut" type thing right about 6k....im guessing b/c its still an auto ecu...but i feel that if would be a direct swap without any negative effects on performance i should do it b/c of the aftermarket ecu's out there.....what do you think?
That's sorta what I meant by saying running and driving you would never know the difference. All of the evap and egr stuff won't effect anything except how much your car pollutes, negligable daily driving mpg's, and an orange glow on your dash.
No, it's not a direct swap. When I did it, both left side fenderwell connectors had to be rewired with the '99 connector (or the engine bay side connectors with '96 spec), everything else is plug and play.
Buy my JWT ECU and that will solve everything. 
96 FED SPEC 5 speed ECU with the 99 NATS mod.
96 FED SPEC 5 speed ECU with the 99 NATS mod.