Would have responded earlier but unable to get on the computer...
The water appears to be being 'pushed' into the boat over the entire transom, not just the cutout for the engine mount. We tried different trims, trimming up seemed to result in the least amount of water but by that time the stern was getting low due to the amount of water already in the boat.
We were unable to get on plane until we got some of the water out by running parallel with the waves, then once most of the water was out we tried to keep it on plane while traveling into the waves. Didn't get as much water in by that time. The majority of the water came in after we left the dive site and were traveling at only around 8-12 mph into the waves.
I know that when the boat shop was initially trying out props, triming the engine all the way in resulted in a lot of water coming over the transom, even on a calm river.
The boat shop is going to move the engine up once I get it in. Maybe that will help fix the problem. This weekend I will install the new bilge pump and see if that helps also.