Fifth Wheel Clearance

With regard to whether you should lower your pinbox or raise your hitch your are better off raising your hitch as long as it does not prevent you closing your tonneau cover as that is less likely to cause problems with the back of the pinbox hitting the side rails of the truck which sometimes occurs with some tonneau covers such as roll-n-lock. The roll-n-lock rails decrease the internal width of the tray by 2-3" either side.

I cannot help you with the trailer height however as either solution will have the same effect on this. As noted by others you may be able to flip your axles if they are not already flipped.