KX 250 bottom end seized?

When rebuilding the bottom end of my 99 kx250 everything is fine until i tighten the case halves bolts. The transmission spins freely until you put any tension on the case bolts...then it seizes solid. It goes from being able to turn with 1 finger to seized when you tighten the bolts about 1/8". Everything is in correctly as far as the shift drum/forks, and transmission and gears. How common do cases warp? Is there a gasket that needs to be used...im using RTV sealant. I've cleaned,oiled,and reassembled this thing like 5 times...im beginning to hate it. Took me 45 min to take it out of the bike and disassemble...going on 2 weeks trying to figure out the bottom end. HELP