I pulled the WP5000 out of its box over the weekend and had a good look at the thing. What I had forgotten about, because I've never used it, is that there is an NMEA connector in the back of the Navigation Receiver which allows the thing to be wired up to a GPS unit. I'm guessing your odd wires are part of this.
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"Those are my principles, and if you don't like them... well, I have others." Julius Henry Marx.