We had a similiar issue on our last 43 DC. The problem was cured with a modification to the exhaust pipes at the stern. We took the boat to Brickhouse boat yard on Kent Island, MD for the work. It entailed accessing the exhausts (8") under the dressers port and stb in the aft master SR. The "tail" pipe that runs from the muffler through the stern was cut a couple of feet forward of the stern and a new elbow was fabricated from exhaust grade fiberglass tube. Large oval holes were cut out of the hull at the proper height on port and stb sides and the newly fabricated elbows were fiberglassed to the hull using very large fillets inside and outside the hull. The exterior was critical because the flow of water needed to be slightly diverted outward therefore the leading edges were shaped accordingly. Mike Stein of Brickhouse did a perfect job of designing the whole thing because when the job was complete we had achieved exactly what we wanted. The exhaust was blown outward sufficiently to enter the slip stream. By the time it started curling back into the vacuum created by the forward motion of the boat, the boat was well forward of it. The only problem with the whole thing was that the exhaust sound was slightly louder to occupants of the aft deck.
Oh, by the way the old openings on the stern were glassed in and finished. A close inspection cannot show that it didn't leave the factory that way.
Walt