Ok guy's - some info I'd like to pass along regarding the Main drive gear bearing, and doing my own research (F.A.G. is dragging their feet).
After removing the bearing in question, I've found that the bearings did not fall apart, contrary to what I suspected, partly because of all the slop on the Main gear, and partly because after the last few trans oil changes I found significant shiny powder and flakes on the drain plug, and in the trans and gears themselves. What I did find with the bearings though, was that the outer row of the bearing seams to have failed first - far worse wear then the inner. The race and balls were pitted on both however. Therefore I have come up with two, simpler, comon and more probable conclusions then bore miss alignment:
A) Fretting or false Brinelling - which is generally caused by small vibrations while the bearing is not in motion. The lubricant is displaced and surfaces no longer ride on a layer of oil. A slow but inevitable deterioration of the surfaces begins. Exponetially. I think this is the most likely cause, and is plausible because of the regular incidence of the Main drive gear being stationary, such as at a stop light, while the bike is not in motion and the engine is running. It's also plausible that the reason the outer row failed first, is that it's further away from the lubricating oil source, and runs dry for a longer period.
B) Brinelling - which is a single over load of the bearings capabilities - causing deformation of the balls and/or races. Also displacing lubrication, and an inevitable deterioration of the surfaces. This hypothysys generally leaves a uniform indent of the balls in the races. Which doesn't seem to be the case here, and the lack of, would eliminate bore missalignment in my thinking.
I can't determine exactly why - outside of bore offset and better production tolerances, that the problems seem to be limited to 07's. Other then a bearing revision which possibly addressed the above problems.
Also it stands to reason that with 07 being the first year for the 6 speed - these problems were new and where dealt with in succesive years.
I'll get some pics tonight for those interested.