What is your Bed rail to the ground height for a FW???

IMHO you need at least 6" bed rail/5er clearance. What you need to now is the height of the hitch plate in the back of the truck and the height of the pin plate on trailer when level and unhooked. This will give you some idea as to your clearance. Flipping the axles is the best choice, but in your case may not be enough. From what you post the dealer sounds a little squirrelly. I would talk to some one at a frame shop.