What can happen some times is when using a roller pilot bearing, a very slight bellhousing misalignment will not allow the trans to pilot. Roller bearings fit tighter than bushings and require the bellhousing to be indexed. Not that it is an absolute you will have a problem if you don't index the bell, but it is common enough to pay attention to if you are having a locating issue and using a roller pilot bearing. If the bellhousing is not aligned to where you can glide the trans into position and you manage to get the input piloted into the bearing, you will side load the bearing and it will eventually fail.
It is too late in this instance, but what I do when I have parts that are not familiar to one another is that I fit everything up and take nothing for granted. When replacing the pilot bushing, I first slide it onto the input to see if it fits correctly. I put the throwout bearing on the collar to see if it moves smoothly in all directions. I put the clutch disc on the input to see if it rides smoothly on the shaft. For new trans and bellhousing, I fit the bellhousing to the trans to make sure the collar slides into the bellhousing and that the bellhousing actually fits flush on the block. A lot of times, you encounter fit issues as you're assembling things and you can easily make corrections, but it just wastes time and is frustrating when you have to pull things down as you're motivated toward assembly.
