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96 gts battery drain

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Now this is what I would do

I would hook up a current meter to monitor the current at the battery(you don't hook it up in parallel to the battery, you will kill your meter). Then, see how much is being drained. If its not much, then it is your battery. If its significant (there will always be some sort of minor parasitic draw) then start disconnecting connections until you find the drain disappearing.

Again, this is assuming the battery isn't defective and just draining itself.
 
Check the Stator wires at the front of the engine. There is a 6 prong plug. It is difficult to get in there without the Seadoo adapter but a little diligence will get it done. Check the 3 wires on the right side facing the back of the ski. You should have continuity between all 3. Then check continuity with the bottom left wire and all three. They should all be OPEN. If you have continuity... the wire is grounded. I say this because my jet ski has a battery disconnect switch.... an obvious eyebrow raiser. When troubleshooting the ski I found a my stator was an issue. I am not sure this will solve the problem but worth a check. Good Luck !!
 
You can also check them at the mpem/regulator.

Edit: not only test them with each other, but test them against ground as well.
 
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