tone,
Curious, is it hitting under the footpeg casting or under the nut? If under the nut, that seems quite far to the outside. If under the casting that seems like it might right itself when the muffler is attached. I just went out and looked at mine ('55 swingarm) and the space between peg and pipe is 3/8". I forgot what year you have, but the pipes are different from '58 on.
This whole topic is quite current with me, because I had the opposide problem. My left pipe was too low and, when trying to fit new standard pattern mufflers, the muffler would pull up on the pipe and remove it from the head by pivoting on the bracket. I did have a local muffler shop put a little bend in the pipe because I thought I had no choice, versus buying another new set. After bending, the pipe was a little high, which proved to be no problem to ease down a bit using an old fork tube in the end of the pipe. I don't know if the bending was made easier by the little tweek bend put in for the correction. If you try this, be careful, as I believe up too high is better than down too low, for the reason mentioned. Though I would have preferred a pipe that was smooth through its entire arc, the result works fine and would only be noticed by our similarly obsessed "Brothers of the A".
Before trying any actual bending, I would try to fit the muffler and see if the forward bracket will give a bit to allow the fit. If it seems like the bracket is going to be overstressed by this, some direct bending of the bracket might work, but be sure to properly brace the bracket when bending, to avoid ripping it from the pipe. (If it is not obvious, I am trying to be careful in what I say, so as not to take you down a destructive path brought on by my advice. Please proceed, as of course you would, with your own sense of due caution.)
One more thing, if your's is in fact '58 or later, seller "queenq" has had a new left pipe on US eBay for some time at about US$89.
Richard L.
