Well I just found the first "hidden" damage on my new to me GS. Aparently the previos owner had let the shifter get loose on the shaft, and stripped the splines almost completely off. The bolt vibrated loose earlier and I got a suprise when I went to shift and the lever was hanging straight down.  Can the shaft be replaced through the oposite side cover, or is this a case split waiting to happen?

I need a picture of what your shift shaft looks like, or what one should look like, before I answer. My first thoughts are about why the bolt was loose, or how it got loose, if everything was working before.

It sounds like the bolt was securing the shift pedal with just enough pressure to keep it from slipping. Once it fell out, the pedal rotated. The bolt is only there to keep the pedal from sliding off the shaft.

If I recall correctly, you should be able to remove the shift shaft from the right side with the clutch cover removed.

The Clymer manual says that the shaft can be replaced without splitting the case. The discussion centers on hard left side drops or wrecks where the shaft is bent. If that, they recommend cutting it off where no bend exists and removing the rest per their procedure out the right side with the cover removed. This also means draining the oil prior to removing the right side cover.

If the splines are not totally gone and the shaft is fair, I would wait until a major need to replace the shaft. Just position it correctly and through drill the shift lever and the shaft. Then use grade 8  or case hardend bolt and aircraft (nylon insert) nut to secure it. Heck, while you are at it. Use the super locktite on the shaft and shift lever prior to installing the through bolt. It will fill any spaces available and make the assembly stiffer.

If you can get miles out of the shaft, use it that way until more work is needed. I'd bet more than one track bike has run that way.

My $.02 worth

The shaft is DONE. I may have another idea though.  :dunno:  If it works, I will take pictures and share. If not, I will hide all evidence I ever tried so as not to be publicly humiliated.  

Oh, as for why it suddenly came loose. There is a very thin row of good spline left at the very end of the shaft. You can loosen the bolt, pull it all the way out to the edge, tighten it down, and it is fine. However after riding a little way, it will slip inward off the spline and slip down. The bolt was not coming loose.

to replace the shaft the ignition cover,rotor,triger plate and clutch cover must be removed, the clutch basket needs to be removed to get to the shifter paw i belive.  ill write in within 24 hours confirming as i have an engine still sitting on the bench with the clutch cover off.

It sounds like the same procedure as most dirt bikes which I have replaced them in before. I have one other idea I want to try first.