I'm finally to a point where I can post an update. Basically, it took the dealer 7 weeks to pull it apart to the point where they could confirm all the damage and write up a work order to be discussed with Yamaha. That's pretty frustrating, but they are a small and very busy shop and this is their busiest season. I expect that they had some issues with techs out on vacation and, while they would never say this of course, I suspect that they were taking care of lots of smaller, quicker jobs that they could do to keep lots of customers happy, knowing that the customer with the big long job was already pissed off. Oh well - they got it apart and have talked to Yamaha, so I'll be happy about that.
There was valve-piston interference, and at least four of the valves are bent. So we're looking at a completely new top end - they're going to replace pistons and rings to be on the safe side. However, there wasn't a lot of damage to the piston crowns, so it's reasonable to expect that the bottom end of the motor didn't experience any trauma, and that there are no chunks of metal floating around in the lubrication system.
Yamaha has agreed to cover the cost of the parts, leaving me with the labor bill. The cost split is about 50/50, so I'm still looking at about $1,500 in repairs. Some of the parts are backordered, and the dealer is still trying to figure out when they're going to be available, so we don't have a solid timeline yet, but I'm guessing it's going to be at least another month before I get the bike back.
I called Yamaha USA's customer service department and talked to the customer service rep who authorized the payment. According to him they were initially going to cover some of the parts, but upon hearing of my experience with my FJR, they agreed to cover all of the parts as a good will gesture. However, since the bike was two years out of warranty, that was as far as they were willing to go. Don't get me wrong - I'm glad they're paying for something, since they weren't obligated to cough up a penny. But I did make it pretty clear (in a very nice way) for Yamaha's customer service record that I thought this was a problem that exceeded "normal wear and tear," and that I probably wouldn't buy another Yamaha without buying the extended warranty, which always feels to me like I'm betting on failure.
I expect that once I get my bike back and am riding it daily again, I'll put this all behind me like I did with my FJR. That said, the moral of this story is that, if the cam chain starts clattering on start-up, replace the CCT RIGHT AWAY, even if it goes away after a second or two. That second or two is long enough for the cam chain to slip and cost you many pennies!
Andrew