I'll try the cut and patch method although I'm not a fan of visible heatshrink... or the bulge the seam may create that is visible through the heatshrink, I should say.
Can you get a picture of the ports? You said that the laptop's USB was right above the coolers, it might help to actually see it.
The cooler is just using the USB's power then I would assume so really you can take 2 of the wires out and make the cable even smaller.
I'm thinking speaker wire or something, maybe even ribbon cable.
I'd like to try and make something personally.
-CollinstheClown