Found a quick fix for my 03 Classic.
Same exact symptoms: wouldn't latch closed, locking bolt wouldn't work as door was too far ajar, no warping, alignment was ok.
There's a faux deadbolt (bottom right, inside) that was zip tied shut.
SOLUTION: Cut the zip tie, lock it. Unlock it.
The door closes/latches again!!
Worried that I'll get locked out by this pesky faux deadbolt. Don't have a spare zip tie around...so I'm using blue painters tape. Bolt to screw next to it are bound together by the tape for now.