Yeah, I’d look at that 6-pin plug as your biggest clue.
If the fuse only blows when that’s connected, it’s almost definitely something in that circuit (stator/wiring/charging side), not the rest of the ski.
I don’t think rectifier would be my first guess, but it’s easy to rule out, just unplug it and see if the fuse still pops when you hook the battery up. If it still blows, I’d move on.
One thing to check that gets missed a lot, test each of the stator wires to ground, not just across each other. The resistance between phases can look fine, but if one leg is shorted to ground it’ll pop the fuse instantly.
Also worth taking a close look at the wiring where it comes out of the mag cover and runs to the e-box. Seems like those can rub through or get pinched.
I’m not an expert on these, but based on what you’re describing it really sounds like a short in that circuit somewhere, most likely stator or wiring before I’d suspect the rectifier.