A few things to check:
- Maybe worthwhile to change the trans fluid just for ships and giggles. I did mine last weekend with Mobil 1 ATF and its smoother than a babys behind. Before this, had notchy shifting when the trans was cold.
- Engine mounts or trans mounts. Maybe if these are toast, it allows things to get misaligned.
Any popping out of gear? I looked through the POs service records and found this doozy at 98kmiles.
"Customer states trans pops out of reverse and second gear." Resolution, Install new transmission, clutch, flywheel, flex disc etc etc. Total damage was close to 7 large. Hope that isnt the problem with yours.