You can add taller shocks. You can change your exhaust. Having a Fat Bob, we have the same stock exhaust which was always common for me to scrape it as well. The Fat Cat solved that problem perfectly with its upswept design.

 

Don't sweat it. Keep riding & scraping, it's no big deal. You have a lot of weight on the bike 2-up, but nothing it wasn't designed to handle. If you aren't scraping something once in awhile then you're not riding the bike even close to it's potential.