Honda Repair: 97 Civic problems, integra motor, civic info

Question
We recently swapped engines in my 97 Honda civic. The new engine has an automatic wiring harness while the original was a manual wiring harness. The car only starts under ether and it won't start on its own. The stereo and everything works. There are a few things from the automatic wiring harness unplugged. What is the problem, and do I have to switch the wiring harness over to automatic in the car to match the one on the engine so it starts and runs? If not, what else could it be? Thanks

Answer
integra motor?
what year?
standard ecu?

i will try to help on this, but it will likely be more that i can do over the net.
and honestly if you try honda-tech you could get a much better answer if you give specific info.
i'm a bit lacking on civic info as i was never really a civic fan. i have a prelude :).