The issues and noise you experienced are exactly the signs of a bad pilot bushing.
You should also check the inside of the input bearing retainer to see if the input shaft made contact with it wobbling around with the extra run out. It probably didn’t with an 833 but it’s not uncommon with more modern transmissions where the input retainer and input have tighter clearances.
I’ll also add that I don’t believe the roller bearing is an upgrade. The bushing will last a long time if it has the proper clearance and a small bit of lubrication, and it should be oilite bronze and not magnetic.
A lot of modern transmissions use the roller bearing, but if it dries up or goes bad the steel bearings will eat the input shaft. If the bronze bushing goes out it eats itself and you get that noise and shifting difficulty, but, it doesn’t take out the input shaft too.