*update*
I reconnected the battery and left everything off - i.e. amps, head unit, air conditioning, fans, etc. - I started it up and drove about 30 minutes, driving pretty tame; for me. At stop lights it was very rough I kept thinking it was about to stall, then it would come back up to idle. Once it got through the rough spot at the bottom of the rpm it ran smoothly and I kept it around 35 mph with maybe a couple touches to 45. Never WOT (wide open throttle) or hard acceleration.
It is still idling rough though.
So you guys are saying that I should just drive it normally and that in a couple days this problem will just work itself out?
Thanks.
P.S. The response to this question has been just great, I put the same post on LS1Techdotcom and even though it got 8 or 9 views not a single person deigned to respond to such an apparently simple question. I love that nobody here is being an elitist auto guy and not getting down on me for not knowing very much about engine mechanics.