FWIW, on the CR250R, a new crank assembly (crank, rod, big end bearing) is fairly inexpensive ($170 or so through Service Honda). I have heard these cranks are hard to rebuild properly, so replacement is a viable option.
Crankcase bearings are about $30, and a full gasket set is around $70 or so. You can get a piston/top end kit for about $120. Shift shaft seal and a few other various parts could run you another $30 or so. I
When I blew mine up my '99, I pulled the motor and the top end off, and paid a local guy like $220 to finish the disassembly and then reassemble with the new parts I'd bought. I thought it was a petty good deal.