Sure it's an Si? When I did a b16 swap into my HF there was a wire going to the ECU that signaled when the car was in reverse. Whenever I put the car in reverse I would get a CEL showing code 6 and would be in limp mode (no VTEC, 7200 rpm rev limit). Just an idea, the HF has a wire for reverse, and also clutch and rear defrost I think. I pulled all of those wires out and the car has run flawlessly since.
In my experience, when the honda ECU gets power/ground on a pin it doesn't expect, it freaks out and displays code 6. Since your wiring is crappy you probably need to go through every pin on the ECU and make sure there's nothing screwy hooked up.