The new fully boxed frames are certainly nice and would address the porpoising problems of the older trucks. I would suggest however that while your truck frame is certainly much stronger than older trucks, the porpoising can also be caused by resonance frequencies of the truck frame, suspension and the road. Even the newer stiffer frames can be effected given the right road conditions.
The resonance issue is different than standard rough road conditions by the way which a stiffer frame will certainly alleviate. I found this resonance issue while driving on some back farm roads where I managed to hit a section of road that had some very subtle dips that were about the length of the truck and repeated for about a 1/4" of a mile. The first few bumps I didn't think much about it but as the suspension and frame started resonating with the road the bouncing progressively grew until the truck and camper were porpoising like a bull in a rodeo.
To get back to your clearance question, I would think that 2" to 3" of clearance is about right if you have clearance lights.
