How have you traced the problem there? Just asking as I have been around the sv motor a while and have not really seen trouble there, seen a bad detent though and several bad shift forks (but I was building race motors).
I would be surprised if the valves went if you kept them to the loose side of the tol. The sv-650 will break a bottom end when over revved on the track, and tends to wear out the cam chain guide in the front jug, and cam chain. I am thinking the tranny would be more likely shift forks.
My original wee (an 04) is in Newport Tn right now with about 138k on the clock and the cam chain is a little noisy as of june( this year last time I saw its current owner). The only thing done to this engine has been valve checks (15k set at max, 65k still in but tighter re-set to max, 110k re-set max loose but were still in).
Just to add to the oil thd(ugh)the 04 had only seen rotella full syn 5w-40 from wally world every 5-6k. (changed when the clutch got a little grabby)
I just did the valves on my 06 at 66,000 (second setting) and could have left them. I just set them max loose again, hint for you guys suzy shims(and aftermkt) are in.05mm increments(7.48mm O.D. shims) trade your shims with an old honda shop, honda shims are avail in .025mm increments. so you can hit your numbers closer(lap them if you really want to hit it spot on).
Valve guides seem to not wear much in these motors in my exp. if the buckets fit properly in the head
Just ramblings don't post much but this caught my eye