The Transmission looks to be in great shape and should be OK as is. I also purchased a used final drive and drive shaft because the splines were stripped out on the bike.
This damage turned out to be the actual problem once the bike was totally stripped down.
Now that I'm working on putting it all back together, I just wanted to up-grade some of the engine parts since it is a 2005 and all torn down anyway.
I did find and buy a NOS OEM complete engine gasket kit I found pretty cheap on fleabay. I have a new clutch nut, Threebond 1207B, and some money for parts.
Looking for the following Up-Grade Parts
Detent Wheel Parts
Lower Cam Chain Gear and Wedge
Cam Chain Guides
Cam Chain
And what ever bearings Warp says I should change while I am in there. (The ones in there now seam to be OK. Yes the Torsional bearing is backwards but it seams to be Ok.)
And anything else Warp says I should change while I am in there.