I'm in the process of rebuilding a VC160 motor as it had knocking due to worn out crank case halves and the bearings moving inside the casing. New bearings installed the fitment was still loose so I centre punched the inside of the housings and use loctite retaining compound to hold the bearing to the bottom crank case housing. On assembly the top half crank case cover bearing would come out of it's position during the installation once I snugged up the bolts it seemed like it went into position fine and both halves gap closed up but the crank would not turn freely.

I was thinking the top half bearing might be out of it's position and putting pressure on the crankshaft making it not turn so I took the crankcase halves apart and centre punched the top cover and added some retaining compound on the bearing and on assembly it looked like it might be good there was slight resistance when turning the crank over but when the bolts are snug it stops moving.
Any ideas what would be causing the problem? Did centre punching the case housing put more pressure on the inside of the bearing making it hard for the crank to move?

The top bearing is a loose fit on the crank, crank is not in the best of shape it has wear on both ends were the bearing sit due to it been being loose overtime. I was trying to keep the crankcase original to the machine but it looks like that might be hard to do.

Nipping up like that indicates there is a lack of end float on the crank for some reason. One of the bearings must not be fully home

Just had another look at it and noticed the top seal had a gap when looking at it from the top side, I just installed it flush with the casing on the inside. Tried hitting the seal further in till it closed the gap on the top side and installed the bearing again and refitted and that solved the issue. I got worried that the case halves had no clearance but crisis averted. Will need to pay attention more next time how far seals and bearings are installed before disassembly.