To diagnose this is just so basic and simple stupid. Start at the easy, eliminate going to the more complex. This is the basics of ANY diagnostic procedure.
Recapping:
Dealer removed transmission and replaced clutch.
Owner DIY replaced shifter.
Diagnosis:
1- Put car in air. Visually inspect and tap, bang, wiggle all the many heat shields and anything that could have been R+Red, touched or banged into during the above. Even what you think as "stupid" or "not applicable". Potential for success = high.
2- Check shifter instal as above including fasteners. Potential for success = high.
3- Then and only then delve into the clutch replacement possibilities of loose fasteners and/or improper installation.
Anybody ever see a diagnostic flow chart ??? You start with the easy most likely flowing down to the hard least likely.
I am sick seeing everyone ignoring the easy basics going straight to the hardest least likely 'I got a bad ______" when after wiping the egg off their faces it was a simple nothing issue.