A few years ago i did almost the exact opposite switch that you did, switching a 500mhz with an 800mhz board in a 12" ibook.
I believe that the extra wires you are referring to are for the modem or the rj-11 jack on the side of the case. As it turned out, when i swapped boards there was no room in the case for the modem from the original to fit on the 800, so there are the modem wires loose in the case and a non-functioning RJ-11 on the side. The laptop works fine, happily running 10.4.11 without it's modem..
Just something to think about.. Good luck with your swap, i dont know what kind of work you will be doing with only 500MHz of G3, but its completely feasible. Also keep in mind that the mount points are significantly different too, but a few of them will line up. I think that my ibg3 is only missing somewhere around four or five screws.
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