i'm going to run the shaft straight out the back, parallel to the bottom of the boat, and connect it to the motor with a flex connector from offshore:

Graupner 1/8" to 4mm flex coupler
http://www.offshoreelectrics.com/products.php?cat=68

this is how the drive shaft is in the aquajet if i'm not mistaken, and that is a fairly high performance boat. i believe the aquajet extreme still ran the straight shaft connected with a flex coupler and it had a 700sc motor and was very quick.
correct me if i'm wrong with any of my facts(i don't have an aquajet[&o])
jarrod