Well, from your first photo the TW looks pretty darn good.
Wheel bearing and seal kits aren't something mentioned much. Matter of fact I can't remember anyone mentioning replacing them, though I suspect someone has. Good call. You've mentioned some good things to check/replace, but you will know more after your shakedown ride.
TW engines always seem to be a bit noisy (i.e. something sounds broken when it's not lol), so if it runs fine performance wise, I wouldn't be overly concerned with the top-end. You may want to check the spark plug for any symtoms of ill running, rich/lean/worn plug, and possibly a valve check/adjustment if needed. You may also want to grease the swing arm.
I'm just finishing up a friends front fork seals, oil, and boots, so you may want to take a look, but from what I can see from your photo, this side looks ok.