Its no problem, the bearing seats against the bottom of the bore, and should be approx flush with the inside of the case. Likewise, the seal is pressed in from the other side until flush, but NO MORE, or it can block the oil hole as gasgasman states.
If you have never done this before, use heat/cold and as little force as possible and never across the race of a bearing. Warm the cases to 250 deg or so slowly and freeze the bearings in dry ice, they should just drop in. I do most of my work in winter so I use the top of my pellet stove but an oven is even better. Post heat a bit to drive off condensation. Before you do this though, ask the shop that fixed the case with the sleeve if it will be a problem, and don't warm the case in a position that could allow the sleeve to fall out.
The crank should just drop in if the cases/bearing are still warm, its not as tight a fit as the bearings in the cases. Again, you could freeze the crank to make it very easy. Just let the crank seat on the bearing inner race.
The roller inner race is done the same way on the crank. The engine shop manual has the procedure, I'm not sure but I think it seats flush on the journal as well.