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So I have a 2007 crf 250r and I am putting the right crank case cover back on it after doing a complete engine rebuild. When trying to put the crank case cover on, it seems to be hitting the gearshift assembly. I don’t have to much experience with engine rebuilding so I would like to know if that’s supposed to be the case or not? When I tightened up the cover bolts a little bit it seemed to close up the gap it was leaving. To me it doesn’t seem right but your help would be much appreciated!

It's obviously hard to tell exactly what you have going on from here. BUT - I want to emphasis to go easy & go slow. We just had a guy hereon the site bust two cases getting a little over zealous. My suspicion is that there is a thrust washer but without getting the manual out to study the diagrams I cannot confirm that. Look it over and analyze.
Maybe Jim will pop in and have some insight.

Problem solved! Gearshift spindle assembly was not aligned with the shifter collar therefor it was causing the gap.

It's obviously hard to tell exactly what you have going on from here. BUT - I want to emphasis to go easy & go slow. We just had a guy hereon the site bust two cases getting a little over zealous. My suspicion is that there is a thrust washer but without getting the manual out to study the diagrams I cannot confirm that. Look it over and analyze.
Maybe Jim will pop in and have some insight.

Thank you for the advice. Better to be sure than to have something go wrong.

Excellent. Good job.