Like Payupp and Derek have said, the engine is dictated by the shaft. Have you ever seen a Correct Craft Ski Nautique? The front of the engine is pointed at the windshield (basically), I just learned all this on the SN I had, and if I remember right the tolerances between couplers was .0003 or less, top, bottom, left and right, between the couplers. On the SN it has an adjustment on all four corners (mounts) of the engine, and it took the better part of the day to get right, and if this process it's not done the shaft can break.
And if the stringers that they are mounted to are not solid, the adjustment will change!

They asked me to help with this project. I know the engine was mocked up once, but they felt something wasn't right.

Thanks for all the input.

If money is no object, you can get a down angled tranny and mount the engine flatter but you prob dont need to. Just copy the original setup.