I'd consider just replacing the clutch disk as a matter of course. They're like 30 bucks from motobins, and SF hills burn clutch like none other.
If you plan on replacing the output shaft seal, I have a hardwood driver I made for the task which you could have (It's located at my folk's house in Mill Valley, just north of you), just shoot me a pm. It may need some more soda can slices glued on as spacers to adjust how it leaves the seal protruding.
Regarding the rings: I think it really depends on the engine. If it runs good, has good compression, and doesn't burn too much oil, I'd leave well enough alone, and do as johhny says: "Ride it till it won't move." Well, you did that once, fix the trans, and do it again. Nikasil bores can be really stable, and likely will still have crosshatching at 100k. Honing them is an SOB, you need a diamond ball hone to actually make any dent in the walls. Otherwise all you can do is deglaze.
When I replaced the engine on my K75 at 100k, it was pretty shot, but I think there was some poor PO maintenance (never buy a BMW from a guy with a Honda PC200), and I also did a 4000 mile tour (with a lot of high speed, high load, high wind riding) with a bad thermostat (discovered later). There was noticeable wear on the cylinder walls and soft ridge formation (feel-able by finger), and the pistons were a fairly loose fit in the bores.