I just rebuilt the motor on my 98 fourtrax 300 and replaced the connecting rod and everything. The problem i'm having is that when the neutral light is on I am in first gear, and I can shift down into reverse but you have to rock the quad a bit to make it go in. It won't shift up past first either, the shifter moves up like normal, but it doesn't pop into the next gear. I'm trying to figure out if this is a shift linkage problem, or a shifting drum and fork problem.

 

Sounds like you put something together wrong in the tranny. Did you try shifing thru the gears before you put the cases together and again right after you tightened the case bolts? You can try removing the shift mechanism and trying to shift the tranny. If that doesn't work, you're going to have to split the cases.