How far in front of your rear axle is your hitch mounted? It seems that the farther back you mount the hitch the more clearance at the tailgate.
I had a 99 Quad Cab, 2500 4x4 that had the hitch mounted about 3 inches in front of the rear axel centerline. I now have a 3500 4x4 that sits about 2 inches higher at the rear than the old 2500. After much trial and error (sitting the rails on the bed floor and setting the hitch on the rails and then setting the 5th wheel pin on the unsecured hitch) I found that if I centered the hitch directly over the axel centerline I had almost the same bed clearance as on the older 2500. I can’t feel any difference in the way the 5th wheel pulls due to the hitch placement. This might or might not be because of the 3500’s dual rear wheels being a more stable towing platform. At any rate, the rig pulls just fine. Oo.
I did not want to lower the rear of the truck because of the cost (I have heard about $900) Also, according to the TSB from DC the over load springs and sway bar have to be eliminated when installing the lowering blocks. I paid extra for the towing package and did not want to pay more money to eliminate it.