Not an expert, but have had a similar problem. The door wouldn't fit on one corner due to the closeness of the roof to the door. Levels still show the body is level, side-to-side and front-to-back. So the last time, I went out and hit the winch motor switch UP really quick and one corner must have popped up a bit (I never noticed it outside), but the door now fit.
So maybe, it is just the top is a bit crooked, and a VERY QUICK HIT OF THE MOTOR SWITCH
Trailer: Lifted 228BH, heavy duty springs and Yokohama tires
TV: 2016 GMC Sierra Z71 4x4 CC, SLT
Spare TV: Two Alaskan Malamutes
Living somewhere in ID; previously lived in Moab UT; previous to that, don't ask!