So, I think this chapter is finally closed! After sending back my original T-5 that would grind going into 5th gear, having them "rework it", sending it back to me, only to have the same problem arise after a few 5th gear shifts, and now finally getting a whole new transmission installed - all is well!
What's interesting is that the shop noted the fluid drained from the old (original) T-5 looked terrible.
Hopefully, this is the end of the story.