I think I really scewed up during initial start up...

Hmm... In that case it could also be the ECU acting up. I'm pretty sure you can't make a 2-pin work on a 4-pin setup, just try swapping the 5-pin ECU you said you have.

Don't worry about it man, your engine should be fine. I just bent a pushrod on my 318 by accident and was worried I messed up my cam or bent a valve... turned out to be fine, once I got a new pushrod!! As long as you didn't touch anything inside the engine and it ran OK before you turned it off it shouldn't be a major problem.