well finally got the final word. The car finally died on my yesterday, took the battery out and got it fully charged then checked all the voltage. 12.xx while running which indicated the alternator, as pretty much everyone has already mentioned. I was so stuck on trying to figure out how the 3 days on jack stands would have caused this problem I really thought it would be all battery related. Turns out it was just a series of unfortunate events that my alternator decided to go bad right after the flat tire fiasco.

Long story short, $60 alternator from a salvage yard and a half hour of work later the battery light is off and everything looks like its in good running order.. knock on wood