Yeah the 98+ suck. If you could get a connector that plugged into those 26pin connectors so you didnt have to lop off the originals, I would be already making conversion harnesses. I have looked EVERYWHERE for a source for the pins/connectors and it seems seadoo is the only source. They get like $4 EACH for the female pins...just crazy.
The other thing is the wiring diagram and the "legend" are kind of hard to decipher. My best suggestion is just start making "your" diagram by wire color and drawing up what you will eventually be connecting.
Its definately doable, but not fun at all when you are lopping off 60+ wires.