Ok so I ended up only having time to take off the moldings on the passenger side last night and I attempted to take pics on my phone so I apologize about the quality.
After removing the moldings and excess glue, I buffed and polished the door with Meguair's which did a great job of taking off any remaining bits of glue.
What boggled my mind is that the rear door was fine underneath the molding when holding up a flourescent light next to it.
Meanwhile the front door had a "ghost stripe" on it. I don't understand how the paint could be lighter underneath the molding. Shouldn't it have been the other way around?
However, the stripe is really only noticeable under the flourescent light and I'll check tomorrow to see if it's visible in daylight. Hopefully 8-9 months of constant, hot Texas sun will take care of it.
Thanks guys for all the advice!