If no other engine lights or codes when you run it, I would still lean toward a supercharger issue.
I am no expert with the superchargers, but from what I have read, they still need to be rebuilt based on time despite what Seadoo says. Think most people are still recommending every 2 years or so to be safe. Has something to do with the plastic needle bearing cages they use which become brittle and fail over time. If it grenades those small bearings get thrown all through the engine.
Since you cannot confirm it ever being rebuilt since 2012, it needs to come off and be rebuilt now. I would take it off and inspect very closely. See if all parts are still there, especially bearings, and there is not play in the shaft. Lots of youtube videos showing ins/outs of these things. If all looks good and no parts missing you dogged a bullet, and we'll need to dig a bit deeper into your issue.