Murph

Okay so. Last month as some of you may remember I burnt a piston. Well I replaced that and the faulty fuel injector. I have had a few minor problems just from putting the engine back in. But nothing I couldn't fix. But I noticed that when the car is idling (for the most part only on a cold start) it misses a beat. Its not loud or anything just a small miss. unfortunately the car has a Bipes ACU timing unit. Which is a piece of ****, I messed with it and got it running a little better. But it still seems to have small misses. So the question is, should I not worry to much, or do I need to upgrade my injectors or rip out the bipes and throw in a mega squirt ASAP?