Definitely worth looking into. I'm almost certain that the wiring for the trackball is independent of any keyboard wiring. It goes directly into the larger insulated cable with no signs of splices, and the keyboard controller's cables enter a bit higher up, again with no sign of splices. This model trackball was used in laptops and other scenarios, so it's very likely that the wiring was kept independent to make the unit a bit more versatile for other applications.
Your suggestion for keeping the wires and just swapping plugs really has me thinking about the possibilities here. I'm pretty sure I've discussed the direction I'm heading and what my goal is as a replacement for this trackball (in the #geekhack chat room). I don't want to give too much away since it's going to be a bit tricky, and it will also be very unique and I'd like to see the idea through to fruition before someone else does it quicker, easier, and better than I do.
When it's all done the board will have DIY cherry reds, (already assembled, i'm missing ONE brown spring! DOH! No scroll lock for now. Anyone have a spare?), a custom color scheme, and some structural changes to make it more "solid" (no, I'm not melting lead). This will most likely be the beginning and the end of my attempts to customize a keyboard to this degree... we'll see how it works out.