I wouldn't worry about submerging the exhaust a bit. My Tartan 30 had the exhaust out the port side at the waterline, and would motor sail quite happily on stbd tack.
I'm curious about the stern squat. More bow/stern wave & slower speed is a sign of a heavy boat. How many drums of bottom paint did you apply? Seriously, how are you measuring speed? Is this GPS speed or is it a calibrated knotmeter measuring true speed through the water (BIG difference)?
It would also be nice to know what you have for a propeller and what you're reading on your tachometer.
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