I think you're on to something with respect to the body shims. Perhaps it was shimmed new and then the doors were installed.
I know that it's fairly easy to torque the frame and body on my Casita
if I crank on the rear stabilizers too much. If I do that, the door doesn't always latch right. A ladder style frame doesn't have much torsional stiffness. Nor does the body for that matter.
As for a fix short of reinserting the shims I don't have any advice. Of course, it would be aggravating to go through the trouble of putting them back and find you still have the door alignment problem.
I suppose my only suggestion would be that if you return to the plywood shim you might try finding some marine plywood for its weather resistance. Another thought is that sometimes you can find a cheap poly cutting board that's about 1/2" thick and cut it up with normal woodworking tools for shims.