Just a quick update on the heat issue. I'm hopeful I may have found the issue, but won't know until I get a ride in a few days from now. I drained the coolant and it appears the PO used straight, undiluted antifreeze. In looking at his maintenance log, it looks like he may have done this fairly recently, mileage wise - within the last 1,000 miles. It was clean, but a very dark green and thick, almost like a light syrup consistency. I first refilled with just water and then redrained, getting more green coolant out with that. I then refilled with straight distilled water and ran the bike for about 10 minutes at an idle with an occasional sustained rev of the engine, letting it get plenty warm and some circulation. More of the green goo drained out.
After the engine cooled, I drained again and refilled with a proper 50/50 ethylene glycol mix. I will give an update after I get it out for a good run.
The bike seems to be running fine otherwise. I'm not a mechanic, but based on this antifreeze issue and a few other questionable things I'm seeing in the PO's work, I've decided its going to be best to take it to a good Yamaha shop and have them give it the once over.