Only 2 things come to mind about rotatating the engine to stop a glitch, something loose on the engine that rubs when the engine is in the down position, or something binding in the throttle cable as its making a different bend. Only 2 guesses that I have.
If you drop the prop down to the MAS 18 x 8 classic, you will find that your boat has a much better take off, handles and responces to turns better and that it will have a faster top end speed, also it will get a better fuel mileage.
If you can at all possible I recomemend any type of muffler. To explain better check out, [link=http://cajungatorairboats.com/v-web/bulletin/bb/viewtopic.php?t=5]tune pipes how they work[/link]