I have powder coated solid disc wheels. They have been on the bike for years. At one point, the bike was either bumped or kicked while parked and a rotor slightly bent. I just lived with it for a while but eventually had the front brakes redone. At the time, the mechanic noted that the powder coating had been done incorrectly and that the surface where the rotor sits shouldn't have been coated as well. It was never a problem before but now the new rotor wouldn't sit flush and he recommended I have the powder coating machined off that surface behind the rotor or I would never be able to completely get rid of the pulsing brake. Live and learn, I should have done it then, but the new rotor (flush or not) significantly reduced the pulsing so I just kept riding. Two years later and now it is really annoying me (and it's not exactly safe) so I am taking the wheel to a machine shop to fix the issue once and for all. Unfortunately, now I cant get the left rotor off the wheel. All the screws have been removed and it's still stuck on there. The rotor is still in good shape so I don't want to do anything to damage it but I really can't get the thing to come off. Does anyone have a suggestion for popping this thing off without damaging it or am I pretty much just going to have to hammer it until it pops and then replace it?

Use a rubber head hammer. You can give it some good whacks to loosen it but not harm the rotor.
If you can, slide a towel or something between the rotor and rim.