Some good answers here. Not sure about the reason for the OP's thin skin, however. Just roll with it; everyone's having fun AND helping you out. Bounce did the best synopsis, IMO. Moving inboards on the bike will get you more turn (shorter radius) for same amount of lean, all other things being equal. Better suspension (FJRs are notoriously undersprung, so this usually means a stiffer spring) reduces compression in corners, the apexes of which are the places you're most likely to scrape. I wouldn't grind off the pegs or feelers (assuming yours are hinged like the OEM pegs) -- that's your canary in the coal mine (and safety margin) that you can ride before the bad hard parts touch down. Practice it on some rhythmic twisties and you can actually do a light touch down from side to side to side in rhythm before you get to the danger zone of levering the tire off the pavement from rigid hard parts touching down.
I wouldn't raise the rear suspension. I tried that on my adjustable Wilbers to remedy the scraping of my Muzzy header (better suspension set-up with heavier spring only real solution to that), and the side effects of the altered geometry are NOT worth it. You don't have to raise the rear very much to get a geometry that has the FJR hunting all over the freeway. Look down or away for a second and you're in the next lane -- seriously. I couldn't raise it enough to make any difference on the header scraping without making it spooky to ride on the straights and went back to very close to stock height to get rid of the nasty lane hunting it wanted to do.
The stock pegs on the FJR are a lot closer to the ground (esp. when leaned) than you're used to on the XX, and you're more limited in how far you can lean it before you start touching hard parts down. Put lowered pegs on it or lower the suspension and you're reducing an already limited margin. If you want to run with the lowered pegs, then there's only so much you can do to minimize the side effects (I think that was the clear message of Ray's freeway post), and you got advice here on most of what you can do already. The FJR with a good aftermarket suspension set-up and stock peg and suspension height is pretty nimble for a big fat sport-TOURing pig, but it's still NOT a sport bike.
