Well, I would be looking into this a little further. Anytime you have bolts that just break off, you will probably have more. Sounds like a salt water ski with a lot of time on it. Ignition timing can be effected by a flywheel becoming loose and rotating on the crankshaft, sheering the woodruff key. It can also be altered by the stator assembly coming loose and rotating. You will have to remove the flywheel to check either of these conditions. You can check the stator coils by testing with an Ohm meter also. You would be checking for damage to the windings from a loose/broken bolt cutting the coil winding by checking for continuity to ground. You say you have a spark, so that may not be the issue. When you were drilling and tapping the broken bolts, the flywheel magnet could have attracted some of the filings and could be effecting your ignition. The other timing issue is induction timing. Rotax uses a rotary valve plate that spins in front of the intake ports, opening and closing them. This plate is driven by a brass rotary drive gear on the crankshaft. You can remove the carbs and, using your finger, hold pressure on the plate while you rotate the PTO. If the plate doesn't move or stops and hesitated anywhere in a 360 deg turn of the PTO, you have stripped the drive gear and it is time to rebuild again. Sorry to be long with the post, just trying to cover most of the bases.
