Since you didn't say what ski it was....
any of the skis on your signature are simple. If you change the stator and the rectifier/regulator... the engine will make power.
I know you say that the battery is good... but that's what it's pointing to.
On the 95 SeaDoo, there is a 15a fuse in the MPEM on the charging circuit. it could be blown.
Actually, all the skis you have listed will have a fuse. Check them.