Picked the bike up from the dealer and it is running well. Talked with the GM of the shop for about 30 minutes regarding my concerns and what the tech went over, etc. Said they checked for vacuum leaks using brake cleaner, didn't pull plugs which left me a little peeved, but they did check TPS sensors and MAP sensors which came back in check to Yamahas specs. They don't replace parts (TPS sensor) unless a proven fault is found and since this appears to be intermittent (throttle stuck) they say its fine. I know I am not the only one who has experienced a stuck throttle so not sure what do to there. No idea on the running hot issue. Might pack a spare fan with me on long trips cause it the stock one burns up, I am in trouble.
I am going to do a TB sync and check for vacuum leaks with propane once I have a chance. It was 94 degrees yesterday and temp hovered at 196 which was what I have experienced as normal. Going to pull plugs and see what they look like as well. Might just replace them. I know there is an underlying problem somewhere. I expect it won't get sorted out unless a mechanic is with me and it happens again. Shop said if it happens again, bring it back (with another diagnostic fee or course). I can't really complain about the shop too much as they had the bike 2 weeks, went over it fully (from what I was told) and did a really nice detail (showroom clean) for $99. They really wanted to help but just couldn't find anything.
So for now, after the post trip service I will do, will ride it until it fails and not worry about it. Next trip Florida to Smoky Mountains in October. With all of the issues I experienced, I would like to know what is the underlying cause. Outside of checking plugs, vacuum leak, etc? Any other suggestions are welcomed. Seems like something really simple causing all of this, but sometimes the simplest things are the hardest to find.
Thanks!