I had the same problem, went from a 2003 Silverado 2500 HD to a 2015 GMC 3500 dually. Not only were the sides of the bed taller by about an inch, but the bed of the truck was higher off of the ground by about an inch and a half. In order to keep my toy hauler nearly level when towing, I had to lower the hitch a notch and ended up with only about 4 inches clearance between the trailer and bed rails (not enough). After some research I ended up having the old spring shackles cut off of the frame and 2 inch square tubing added, then remounting new spring shackles on the new tubing. Also had cross bracing added between the new frame mounted tubing. My axles were already below the springs, so "axle flipping" was not possible. Trailer is now level when towing, and I have just under 6 inches of clearance between the bed rails and the trailer. I looked at using the billet aluminum spacer blocks being sold by a Canadian company, but I was not comfortable using those on a 15,000 lb., 35 foot long toy hauler. Probably fine for a lighter, smaller trailer. Not too many options out there short of removing the bed and replacing it with a flat bed.