Went through the transmission last year when 2nd exploded. Bike has been running well since until it wouldn't shift into second or third sometimes. Started happening while trail riding. Shifts ok when standing still. Anything to look at b4 cases get split again!

 

I'm assuming since you have split the cases once before, you have checked all the minor things:

cable adjustment at case and lever.
oil level and possible leaks.
shifter pitch. is it tight or loose on the shaft?
chain adjustment.
what sprocket sizes are you running? I found with a 12/44 setup the bike did not occassionally did not like shifting from first to second. since switching to 13/43 I have had no problems.

 

did you upgrade to a 02 trans? did you replace the shift drum?

 

Did the easy checks first. There is an 02 upgrade in ther now. The shift drum was not changed. What should we be looking for?
Not sure what a shifter pitch is. Thanks for the responses.

 

How's the clutch?

 

Clutch is good. Replaced when tranny rebuilt.