Sat for 3 months, now its running rough.

The car has sat for 3 months. When I went to start it the battery was dead so I jumped it. Start right up, no problems at all. Ran it for about 30 minutes to charge up the battery then shut it off. I waited 10 minutes then started it back but and the car surged to 2000 rpm then dropped to 800, ran rough, fluctuating between 900 and 500 at an idle. It runs clean at above 1800. I was thinking maybe the fuels gone bad or a blocked fuel Injector. The fuel was not stabilized before storing. The other possibility I considered was a bad battery/alternator. While it's struggling at an idle the interior lights flicker.