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hmm, it looks like RetroPie 2.3 has been released since you started the project.
Would it be worth using that?

I’m afraid I’m not that experienced with the old version – I have a guide of how to hook up the controller, but I’m not sure how to go about it with the GPIO setup.

Using the autoconfig will import the file that retroarch generates, but again, all the path references I would use are relating to RetroPie 2.3

I’m pretty sure the GUI screen you show above can be manually edited in the retroarch.cfg file – so you could find that in your local install. If you use 2.3 I can help more with paths.