I had an alternator go out on my Truck one time. Went to NAPA and got a new rebuilt one.. Got it installed and several things like idle control and some others items were all wrong.
I always thought thing would relearn themselves but after a week of dying everytime I took my foot off the gas pedal I final went to the Ford place. Cost me $90 to reset my computers settings again. Took about 5-minutes on their machine. All was fine after that geesch...
Maybe being unhooked from your start battery system for a long time to get your work done has done something like this to your Engine Electronics settings???
Roy Ken