Pics later when I get a good camera. Also how could I wire up a external gamecube controller port?

If you don't even know how to wire up a controller port, then you're going to have a hard time finishing this.
To answer your question:

This is the controller board. Just desolder one of them off, or leave it on the board, your choice. Then, wire it up to the board (only if you decide to desolder one of them) or just keep the controller board connected to the motherboard. You're going to need a switch to flip between the two data lines; the one coming from the internal controls, and the one coming from the external controller.

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Just never mind I have it all sorted out.

Where do I get some jb stick?

Use epoxy.

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I'm entering the race: My µGC Worklog (WIP)

JB Stick: http://jbweld.net/products/jbstik.php
JB Quik: http://jbweld.net/products/jbkwik.php
JB quik aint bad at all, but only use it for filling major pits in your case. You could prolly get those stuff from your local walmart or something.

Nahh, I tried that and it didn't stick very well...

Yeah " ." doesn't tend to stick very well either.

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I'm entering the race: My µGC Worklog (WIP)

Haha, oops.
Anyone know where I can get some decent 1- or 3-party that don't break when cutting traces and relocating stuff?

Almost nothing will not break when you cut it's traces.... It's only a matter of rewiring it correctly. eBay is your friend. Dealextreme Is your best friend. Search them for some GC controllers.

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