Anyone with experience in old BC type gearboxes
 

They used to be notorious for the diff bearings going, and back in the day I replaced many the bearing. However, in my 1990 XR2i, I changed the input shaft bearings, and the diff seals. No biggie, but when I put the casing back together, each side didn't sit flush. It was as if there was something stopping them from closing together. I can close them if I tighten the bolts, but should that be the case? It's so long since I opened a BC gearbox I forgot if this is normal, and if tightening the bolts just sets the preload on the diff bearings. I've stripped the box back a few times since in case I'm missing something, but I can't see if there's somethinmg wrong. If I leave just the diff in, and close the casing by tightening the bolts, the diff becomes harder to turn, but if I have the gears in, I can turn the input shaft by hand, and the diff is turning, but if I go with it as is, and it's wrong, those bearing won't last long. Any advice?

Seems not

Ive never had to use bolts to pull the housings together. A light tap with a rubber mallet yes but once down i didnt need bolts to "hold it" down as such.
When you say diff seals, do you mean driveshaft seals? As they wont have any impact obv.
If the input shaft bearings aren't seated all the way to their correct location however you could be essentially forcing the entire shaft downwards when tightening up and this is binding against the other end of the housing.

Thanks for that. I stripped it back a couple of times and couldn't see any reason why it was binding, so I left it open until I found out if it should be pulled close with the bolts or not. I'll have another look again so. Something must be wrong somewhere