there are specs for the resistance of the coil and stator ohm readings in the manual.
are you sure its coming back out of just the mag carb? on an x4 or 3 seater 787 ski, you could mark the pto for TDC and check the timing with a timing light.
another thing - has this motor been hydro-locked before? since the crank is pressed together, if one cylinder gets locked, and the rest tries to keep going, it can get the crank out of phase so the timing isn't right on the inside even though it seems right on the outside. the test for this in the manual is to take a longish and a shorter screwdriver, and get one cylinder near TDC so the other should be near BDC. put the screwdrivers in the cylinders and rotate the crank by hand, looking to see if anywhere in the rotation both cylinders are going up or down at the same time, indicating the crank has slipped.
also again double check that you've got the fuel lines routed in the right direction and on the right places and all, and that the pump pulse line is in good shape. you might also think about hopping on ebay and getting an oem airbox and flame arrestor screen setup to get some consistency to your tuning challenge.