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12.2 is not enuf Battery voltage for the IBR system, the IBR module will tell the ECM uh uh, and the ECM will throw the code. So your new battery is bad, your charging system is bad, or the battery has never been fully charged. Take it out and charge it to full capacity and then have it load...

Absolutely make sure your battery is good, take it and have it load tested.

Try a new 30 am relay

Im voting for not charging, you need to find what caused your fuse holder to melt. Download a service manual and trouble shoot the charging system.

Test your rectifier, the diodes can go bad and allow current to flow the wrong way in the charging circuit, causing all kinds of weird issues. Although it now sounds like you blew a main fuse.

Sounds to me like you have high resistance/corrosion somewhere causing a voltage drop at lower RPMs below the safe operating voltage range of the IBR system and the IBR module is telling ECM which then throws a fault and limp mode. Double and triple check all the wiring, connectors, and grounds...

Stock prop

You Tube

Probably go with the Seadoo recommendation for the second battery.

Secondary Battery Harness Kit 295100991 - Personal watercraft | Sea-Doo - USA Not sure why but it doesn't fit your ski, dealer would know more.

Very good then, the proper sequence should be for the ECM to power down the ski 15 seconds after it notices there is no key on the dess post. Your issue is not common. The dess post switch is sticking closed, the start/stop switch is stuck open or closed, or the ECM is toasted. I am a little...

Was the battery connected to the ski while being trickled charged since last summer?

First step with electrical gremlins is to make sure your battery is good, take it out, charge it up and have it load tested.

You should be seeing "enter level" not "enter speed", "enter speed" is what you should see when setting the speed limiter mode. From your manual "To exit the selected speed control mode, press MODE button or long press SPEED CTRL button." or your speed is above 9mph when trying to enter the...

What happens when you wake up the ski with the start/stop button, put the key on the dess post (2 beeps?) and then try to start it?

Probably is a repercussion from being sank, how long was it under water and how long did it sit sit before it went to the shop? Was the shop a Seadoo Dealership?

A 3M marine epoxy with a filler, they have different fillers for different jobs. West Marine has knowledgeable associates if you have a store nearby. I have used it to repair damaged hulls on small sailboats. Stronger and waterproof which fiberglass is not. Gel coat after the epoxy. Any cracks...

A small battery BMS is designed to protect the battery it is managing, not the vehicles electrical system/charging system the battery is storing power for. By protection I am referring to a system to help prevent the battery from catching fire and burning up the vehicle its storing power for so...

Engine Charging Systems With Lithium Batteries | Fact Sheets Good article, if you scroll down it talks about the Rotax charging system and Lithium batteries

One plus feature of LiFePo batteries is their ability to accept higher charge (C) rates than lead acid batteries. So usually when an alternator or magneto charging system designed for lead acid is put in the picture even with a BMS, a DC/DC charger is used to limit that charge rate. Seadoos...