I guess no one wants to tackle this one, probably because there could be a lot of different issues. One thing I see is that the legs & knees must work at absorbing the bumps, not only to minimize the pounding, but to keep the board on the surface of the water.
Keeping everything straight and vertical is fast, but it's also rough on the body. Longer harness lines might let you get further away from the boom and "hang over the water" more. It used to be cool to have really short harness lines, but many of the top racers are now going longer.
I have back problems so I do a lot of exercises (core muscle work) to prevent strains. I also were a fabric weight lifting belt for lower back support. I find that this works well when there is a lot of pounding. I have never used a waist harness and love the seat harness. If your "things" are getting squashed, try something like a speedo under your swim suit, it will keep them out of harms way.
Others may have some different suggestions to help you out.