CR125 Transmission is hard to turn, crankcases seems difficult to get together.

So I finally started to put my 125 motor back together and ran into a problem in the early stages. First I'll tell you what I did; All of the engine is ok, except the crank but I bought a Wiseco bottom end kit so I decided to swap out the main bearings too (the engine was only 4 hours old, except for the crank). Anyway, I froze the main bearings and lightly tapped them in til the sound changes (you know how the sound changes when you tap them in). So then I put the transmission in (with the shift forks in correctly) and everything seemed fine. The crank went in alright too, so I put the other half on and lightly tapped the cases down (note; I checked the cases for warpage, 100% unwarped). So drop the bolts in and just seat the bolts down (not even torqued down) and check the crank for movement - fine, check the transmission - really hard to turn. So I remove the bolts, and split the cases and check the transmission - turns fine and all the washers and stuff are in. Although I notice the right crank case half appears to have grind marks from the countershaft. So I check the main bearing was incorrectly and it won't go down (this is on the left crankcase since I thought the bearing might have come up. I put it together and apart a bunch of times and the same thing happened. When I lightly put the cases together, it feels like the case is pivoting on the crank.

So I'm starting to wonder if the Wiseco stuff is correctly sized. Last time I used the genuine Honda bearings and everything went together (I had no idea how old the crank was but it was still in spec). But last time everything went together so easily.

Any ideas why tightening the crankcase bolts would seize up the transmission upon tightening? I'm thinking I might reuse the old bearings (like I said, 4 hours old) because they're still in good condition. But it's a pain to have to remove them.