[BrickPig]

Car idles around 500 rpms when at a traffic light and in gear....

From your description I'm guessing that you have an automatic (because you say "in gear").

I'm further guessing that if you are stopped and the car is put in Neutral that none of these problems happen?

If so, then I think the idle is set too low, and/or the switch/mechanism to kick up the idle when the AC compressor is working is not functioning. 500 rpm seems kind of low...

 

[BrickPig]

I unhooked my battery when painting the rear rocker panel on my car and didn't want the battery to die with the door open.

Just FYI, our cars have an auto shutoff that turns off the dome light when a door is left open after about 15 minutes. I've worked on my car with the doors open for hours with no ill effects. The power is restored when you close a door. There is also a manual switch to turn off the dome light.

Not sure if the auto shutoff will also turn off our headlights after 15 minutes...haven't had the guts to try that one...

 

[BrickPig]

The clip below the battery for the fan looked to of been messed with and it was barely seated and pushed on in the wrong direction.

And now the question is: how did THAT happen? I can't believe it came from the factory that way and you didn't notice it for 60K miles. Sloppy maintenance? Hopefully it wasn't done by a dealer...because then there would be no excuse...