I've noticed that the drivers side rear sits about .5" lower than the passenger side rear. I'm thinking this is due to the muffler and sub being located on the drivers side but wanted to see if anyone else had the same issue

Yep, on my SS/SC and it was the same way on my '91 Formula. Every now and then I'd come out in the morning and at first think I had a flat on the driver's side.

my driver side is lower to. i thought it had something to do with me removing the front tire to get to my airbox

Did you ever consider the DRIVER has something to do with it as well? If you're always the only one in the car, then the driver side is always taking more of a load than the passenger side. It just means the struts are settling more quickly becuase of the consistent load. I wouldn't worry about it though. Eventually they will both balance out. Expect the suspense to settle about .5" lower as the car ages.