Attach a voltometer to the battery with the ski off. record voltage. should be 11.6 to 12.4 ish.
start the ski, test voltage again (you did hook it up to water right?) at idle or anything higher you should be seeing power levels HIGHER than with the ski off. usually 14-15v. anything higher or lower means you have a problem.
it's either the stator or MPEM.
I replaced my stator last year. a ohm meter and the sea-doo magneto plug tool will tell you if it's the stator. (or a 1/4 hr labor at the dealer).
because the tool that plugs into the stator is like $30... for how many times you will use it...? meh.