I want to remove the door to get some minor body work and paint done to it. If I remove the 6 bolts that hold the door on to the hinge, will this screw up the alignment when I put it back on.
weel, yes. All the adjustment in the door is done at that point.
It's not that hard to readjust though.
You could also mark where it is at with a black marker, then just realign with the tracing when reinstalled