What type of hitch do you have? A plate type or turnover ball type?
I've only installed a gooseneck on one truck with a body lift, it was a B&W turnover. I refused to modify the hitch itself for liability reasons nor would I carry the warranty if he modified it afterwards. He ended up cutting about a 6" square around the hitch in the bed so the neck of the trailer could actually sit down in the bed a bit and properly sit on the hitch. Honestly I thought it looked like crap, but I feel this is the safest option as you are keeping the hitch in it's designed location.
Your other option is if you or someone you could take it to is very comfortable in fabricating & welding. You could always more or less make yourself new rails across the frame with steel tubing to accommodate the height difference with the body lift... But honestly out of the hundreds of 5th wheels and goosenecks I've worked on I have rarely seen any home brew work that doesn't make me uncomfortable when I see it.