Spent a couple of hours trying to install passenger footpeg brackets on my 2012 Nightster to find out they won't work with my Akrapovic exhaust. Wife is not happy with me right now.
You could take the exhaust off and try to clearance it right in that area. I have seen others do this with the V&H Comp pipe. Done right you may notice but it still looks aesthetically pleasing.
Edit: You could also try and clearance the foot peg mount.
^^^^ that's not a bad idea except the foot peg wouldn't fold down it would sit directly on top of the exhaust. I just kind of wonder why akrapovic didn't design it to go under a passenger foot peg.
Best advice I can give (and it may not be the advice you want) is to sell the akrapovics. Most instances I have seen them installed they have lost 5-8 HP over even decent slip-ons.
@Austin I bought the bike new from the dealer with exhaust already installed. I made that suggestion to the wife and she didn't like that either lol but that's what I was thinking. @mj I had them flipped but it stuck the peg through the exhaust pipes and the pipes didn't hang correctly. I might be willing to trade them out with someone if they had similar value pipes.