I have a 5spd integra (98), I might be getting an excellent deal on an automatic shell thats in mint condition (way better condition then mine) I was wondering if i did the auto to manual swap if I could just swap my manual harness into the auto instead of cutting the auto harness. I've looked online and I haven't read much, if any, information on this.
Well it depends on the year of the shell. If it's 95 or newer, than it's obd II, same as your 98. So you should be able to swap your 5 speed harness, and then you also need to use the 5 spd ecu.
You should be able to swap out the wiring harness without a problem. Might be a bit of a headache but be sure to take your time and mark where everything goes. Take pictures if you can and use masking tape [folded over the wire and onto itself] to mark the various connectors.