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.
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.
I broke my regulator board 12v line by putting my soldering iron on it too much and the contact flaked off. This is really gonna set me back. But I got a $25 Pre-paid Visa debit card so I will be buying stuff soon.
Update: Got my controller a month or so ago...... Sorry I haven't updated this thread in awhile so..... Also I need some money to buy a dremel, so..... No further updates till I do something else, which will be most likely in about a month or so..