Here is the procedure I used to align my engine/pump.

1. Take pump and remove plastic end seal. Use graphite pencil to get graphite on end of pump. (You also could use a piece of carbon paper) and put it nose first down on a square foot of 5/8" plywood.
2. The pump body will change position if you touch it. You want the pump body to stay in one spot and not rotate. Put a 3" screw into the plywood as a stop for the pump body so it does not turn.
3. Use a new wood pencil to carefully mark where the holes are that are used to mount the pump. There are four of them. Keep the pencil as straight as humanly possible, do not let the pump body rotate as you do this marking.
4. Drill out the four holes to the same size as the mounting bolts. Make sure you center the hole exactly. Use a pilot drill bit first.
5. Stick drive shaft into pto flywheel. On the pump end of shaft measure how much play the shaft has from side to side or up/down (either one). Measure this carefully.
6. Go back to the board, add 1/2 the play measurement to the marking made for the shaft/pump hole. Find the center of hole and use a protracter draw a hole that has an outer edge equal to the original marking plus 1/2 the play measurement.
7. Measure how big the hole is and use a hole saw to cut it. A jig saw will not work.
8. Mount the piece of wood where the pump goes. Install drive shaft. The engine is basically aligned when the drive shaft touches all the outer areas of the hole.

I bought an aftermarket drive shaft for my 1996 GTI . The splines were straight, not cupped like the OEM Seadoo. I stuck the drive shaft into the PTO and at the other end there only was about 1/32 inch play. It was not neccasary in my case to enlarge the hole. The drive shaft end fits snuggly into a 3/4" hole.

The Seadoo drive shaft is cupped on the spline edges. This makes it a no brainer for people on the assembly line to throw it together. I really wonder about the tolerances for alignment given the driveshaft spline design.