I had this same problem, but luckily I happened to notice all the problems while I had the chaincase apart during my Cat skid upgrade. The bearings were trashed, and extremely loose. I bet one or two more rides and I would have done serious damage. That was at aprox. the 3000 mile mark on my second season. I wouldn't say you guys had any particular problems, just typical wear for these machines. I have a feeling more people have worn chaincase bearings than they think, but the opposite side jackshaft bearing gets noticed more easily because its out in the open.
As for a real repair...I can't begin to guess. Replace them, put new oil in the case, and ride on...and keep an eye on the new bearings. I can't give a really educated opinion about reusing the chain and gears, but my personal opinion is to check the gears for signs of damage, such as chipped or gouged teeth. Check the chain for looseness the way you would check any chain...try to bend it sideways and see how far it moves. If it bends a lot, it has a lot of wear. If it doesn't bend much, its probably fine. Also visually check the inside of the chain for signs of bent links, chips or other visible signs of damage. If everything looks and feels fine, you are probably O.K. running the chain and gears. These chains are pretty durable, and can take quite a bit of abuse. Clean the chaincase out really well and run it.
Jim