Huh. I hadn't thought of this before, but it should work. The waterproofing is the only potential gotcha, but a simple wrap of duct tape and/or some vaseline or similar stuffed down into the connector would take care of that right quick.
I see these types of cables at thrift stores frequently, usually on chargers but sometimes as separate USB cables. Then I just need the female connector, which I can probably get out of various dead devices I can ask for on CL or Freecycle. Pretty sure i have a couple of them already, so once my house/yard cleanup project is done, I'll probably take a look around and try this out. I'd definitely prefer this kind of thing to the existing JST connector, or any of the others.
But there is one more connector that will fit thru those nuts, with little modification: The PS/2 keyboard connector. and they come as extension cables you can simply cut in half to splice to your existing wiring...I did this on DayGlo Avenger for the Fusin's first installation, and it worked well, although I hardly ever cycled the connection. Then if you need longer wires, you can just use another extension (intact) to do so.
You'd have to trim off the shoulders of the grip portion of the connector, most likely.
The only catch is it *has* to be the first connector thru the nut, and the last one out.