Another reason I wanted to keep the sides of the transom the same height was so I could mount a kicker motor directly to the transom like Bondobill's setup. Right now it measures around 20 or 21 inches right around where the scuppers are and a 9.9 or 15 hp long shaft motor measures 21.5 or 22 inches. That way I can have the security of an auxillary motor but don't have to mount one of those drop down brackets. Thoughts?
In regard to your scupper woes. I owned a commercial model Sea Ox before my current sport model. It had the same set up as your Aquasport. The little scupper holes were in the stern. What I did was glass over the stern scuppers and relocated them to the sides. When you build that well, put the new scuppers where the end of the well wall meets the hull. They will be about three feet forward from the stern depending where you have the front of your well. That will get your scuppers way up above the waterline instead of sitting way below the waterline as they were in the stern. Worked really well for my Sea Ox. I used a 3" hole saw and cut the scuppers out on the side of the hull. Then I inserted threaded PVC. When it gets rough you can screw in caps into the scuppers to keep water at bay.