Bummer. Just came across this.
I'll keep my mouth shut for the most part. Most advice has been excellent, and you have decided on your path.
I am not a mechanic, nor do I play one on TV. Nor am I a Yamaha engineer. I get my valves checked on a regular basis. I have just recently started extending my interval to 30-32k miles based on the 8 or 9 checks I have had performed on my FJR already. That's my choice.
I have seen and heard of many skipping or greatly extending various maintenance FJR maintenance intervals (me included) on this forum. I think a lot of these folks are nuts. I would not want to buy a used bike from a lot of peeps on this forum based on what they have posted.
Not to say any of this means squat in Mike's case.
I will say I think there is an issue with the FJR's #1 cylinder. In Gen Is, that is usually where the problem came if it was a ticker. In my own old 226,000 mile FJR, the last valve check that was done showed a leakdown test loss in the #1 cylinder. Based on the air coming out of the exhaust valves, my knowledgeable tech suspected a wallowed seat for one or both of the exhaust valves in the #1 cylinder. Most likely to to worn valve guides. Or in other words, a ticker that took 200,000 miles to manifest. (It didn't tick - it was quiet) Still, I had no oil consumption or loss of mpg. Power? Maybe a slight loss of power but with 220,000 miles on the clock I would expect a bit of a drop off anyways. BTW, compression in all four cylinders was within spec.
So, my total SWAG is that the FJR, perhaps only Gen Is, has a 'gets too hot' issue with the #1 cylinder.
Best of luck Mike. Though it may be a bit spendy, I am sure she will be better than new when you get her back. If they are not going to do it already, I MOST DEFINITELY would have them install the newer, updated Gen II valve guide seals in your head.