Executive summary about cr250 parts by myblazeofglory
First remove the 3 bolts to the sub frame, loosen the clamp on the air boot, and remove the sub frame and air box as an assembly. Leaving the 2 radiator scoops on the gas tank makes removing the front easier as well.
As soon as I removed the top end, I could see that my suspicions about the right main seal were correct. If you look closely you can see the pool of gear oil under the crank. A bad seal usually indicates a bad bearing since the bearing usually goes first taking out the seal as the worn bearing allows additional movement. The entire crank assembly and connecting rod will be replaced as a single unit.
To measure the cylinder first determine the specifications. On a 2001 Cr250 it should measure between 2.6141 and 2.6144 with the service limit being 2.615.
The piston on this bike should be between 2.6114 and 2.6117 with a service limit of 2.609 with a clearance to cylinder service limit of .09.
I have known that the bottom end was going bad for a while, but put off the rebuild a little too long. The signs include excessive smoke and spooge at the exhaust from burning gear oil, the noise as described above, and having to add gear oil excessively.
Make sure the transmission is installed as shown with the forks in the correct grooves of the shift drum. Assembling the parts on the other side of the drum is tricky, you'll want to install the shift lever temporarily at this point to make sure you can shift through the gears, then install the outer clutch basket etc. in reverse order of how they came off.