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I've got two 98GTX LTD and see similar problem. Easy thing to do is get a voltmeter and measure the DC voltage across the battery while revving engine at 5500 minimum. In your driveway is fine for just a few seconds. Don't try in the water! You need to be greater than 13-13.5 volts to charge battery. If not then the rectifier in your MPEM is bad. If you are seeing greater than 15 VDC then again your MPEM is bad.
If you are not getting your SeaDoo up to decent RPM while using then you are not going to keep batteries charged.
My problems came from wife who likes to do a lot of stops and starts and not going fast in between. Eventually she can't start out in water. Pull it out of water and it starts right up without the water pump loading it down. I bought a small capacity trickle charger for each and hook up the batteries while they sit in garage. By the way if your SeaDoo is off and just sitting around it is still drawing from the battery. If you want to save battery then disconnect the negative terminal while not in use. Bad news is clock is never right. Another thing you can do is start it up briefly while out of water before launching because a cold start always takes more starter cranking time. If you try a cold start in water then your pump is making your starter work a lot harder thus sucking more current/stored energy from your battery.
This is not coming from a SeaDoo mechanic so take it as experience only. In the service manual it describes how to precisely check all of the charging circuit. You can get one on ebay for $10.
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