Idle surge and stalling

Ok a little history before I get to the problem. I trailered my car to kentucky a few weeks ago when I got here and tried to start it the alternator was fried. I couldnt get a new one right away so it sat for about two weeks i finally put a new one on and now when I start it the idle surges from 1100 rpm to 500 rpm for about 5 minutes before leveling off at around 750 rpm. it never surged that much before and im not sure what rpm it used to idle at i never really paid attention. after i drive it for a while the lope seems to change at idle sometimes it sounds fine sometimes its really choppy like it wants to stall. and if I cruise at highway speed for a while then push in the clutch it dies sometimes. I cant figure out if it's a fuel issue or if my idle is too low. if anybody has any ideas that could help or if you need more details let me know.

Thanks
Joe