Like the topic says it wont come all the way out. The very end of the shaft seems to be ever so slightly larger then the opening in the case. Is it ok to jsut file material off the shaft untill it clears or is there something Im missing?

what kind of trans is it? what shaft are you having a problem with? main shaft? shift rail? etc etc. need some more info.

Oops

Its a stock 700-R4. I removed everything else hooked up to it but the end of the manual shaft (the shaft that the shift cable hooks up to) wont clear the bore in the housing and slide out.

A burr is typically raised on the shift shaft when the detent plate is tightened on with the nut. When you take the plate off to remove the shaft, you need to take a fine file and dress down this burr, before removing the shaft from the case.

Thanks... I got it out.