Got the case apart. It was an absolute piece of cake, came apart virtually by hand with a few taps on the crank shaft and gearbox shafts with the rubber mallet. The problem is that the shift forks are completely stuffed. The lobes on the ends of them have been worn/burnt off completely hence the shifting issues. Also, the two right side bearings, the ones on the end of the input and output shafts, are pretty average. Im going to replace them. It is interesting to know that these forks are the weakest link in the package when it comes to riding the bike without any tranny oil....the heat built up burnt the lobes right off. I am happy to post some photos of them if people think it will be useful.
This job really isnt that hard at all, anyone who is considering splitting the case to do gearbox work or replace bearings should go ahead and do it. The shops charge like a wounded bull for this work, you could save serious money.