Wondering if anyone has had problems with their MT82 Mustang manual transmission?

I noticed problems at ~244 miles when I picked up my car from a Ford dealership, Bozard Ford, where it was in for warranty repair of fender/door misalignment which caused paint damage. After a poor paint repair by an auto shop, video below, I brought my car home from the dealership, and when I drove away in my Mustang after the dealership had it for ~16 miles, I immediately noticed the manual transmission didn’t shift right at all (it always shifted perfectly when I dropped it off). The transmission would basically now bind, catch, grind and then pop into 4th gear at low RPMs in a very odd two stage process. It absolutely never did this before I dropped it at the dealership. In addition, third and fourth now made a louder thud going into gear. The transmission shift quality was significantly, noticeably degraded somehow when I left it in the dealership’s care.

Does anyone know what would cause this really poor shift quality? What type of condition? What should I do?

Door hits fender:
Poor Paint Repair: