So, after a week trying by myself I gave up hope of getting it done :-(
I can’t seem to get my NES-controller working with RetroPie…
I CAN get it to work with the WiringPi package, but not with gamecon or snesdev.

Im using other pins on the GPIO as pre-scribed by the RetroPie package. I’m using the following pins on my rev2 board.
P1: 3.3v
P5: Data
P6: Ground
P11: Clock
P12: Latch
These worked with the WiringPi software.

Is there any way I can change the pins to be used by gamecon/snesdev?
Second question: is there any NES-controller driver, not integrated with the RetroPie package, that you guys know of?

Any help will be greatly appreciated!