I agree, in stock form, the FJR's cornering clearance is an issue. I noticed it the day I bought the bike.
I started off cheap and bumped the preload up in back as far as I could, first with the lever, then with a preload washer. (The guy who was making them isn't any longer - they're still a few floating around though and it's just a simple fat washer.) With the preload on Hard and a 3/16" washer, my bike is marginally acceptable - I stil scrape now and then, but I seldom want to press any harder on this big/heavy a bike. But at the track, it would still be totally unacceptable; fortunately, I have other bikes for the track.
Next step would be a firmer spring. There's a couple outfits making FJR springs for the stock shock, or you can get a new damper too. On other bikes, I've loved Ohlins and will go with this if I decide to keep my bike long-term. A lot of folks here like the Wilburs.
I haven't tried the new dogbones, but this is a good solution on many bikes:
https://www.whaccessories.com/YamahaFJR1300accessories.htm
I'm not aware of peg-raising kits and wouldn't recommend them if there were. As soon as you raise the pegs, you're going to start hitting something else: exhaust, centerstand, etc. with more serious consequences. And, of course, you'd lose legroom.
- Mark