I have noticed a few times recently when going over bumps in the road that there had been a real clunk in the right foot peg.  I couldn't work out what it was, but..

When cleaning the bike the other day I saw that there is a patch of paint rubbed off the right forward control footpeg mounting bracket where it comes close to the header pipe.

Is this normal? Is there possible a problem with a loose engine mount or something which is allowing the engine and therefore exhaust to move around too much?

Could this be a warranty issue I can claim to get the mount repainted / replaced?

I'm about to install a set of V&H big radius, and I don't want the rub mark to be visible, and I dont want it to rub on the new pipes.

Sounds like a warranty issue to me mate, quite surprised that it is hitting though?

it is common for the engine mounts to rattle loose on the 48's

check em

once a week a quick walk around with a set of spanners, bit of a nip and tuck over a Sunday arvo beer, as yet, I haven't had anything loose enough to worry about, but the check is quick and easy, and the added nip on the nut isn't going to hurt.