Update:
Pulled the fender, re-hung the door and then re-hung the fender. It wasn't easy (took nearly 3 hours) but it did help me get the door lined up. Now all i have to do is get the fender back right....
I've got about 3 bolts that still need to get put in to connect the inner and outer fender in the wheel well. Any tips on how to get them lined up better?