first thing i'd do is loosen the bolts that secure your headerpipes to the cylinder heads. also slacken the pipe clamp that mates the rear header to the cross-over in the forward header. give the whole system a couple light taps with a rubber mallet to loosen it up. then install your high-mounts, align everthing so it looks right and clearances are ok, THEN tighten down all the bolts/nuts.
good luck with the swingarm. i doubt you'll get any lovin, but there's no harm in pointing it out to your dealer to see if there's something they can do.