I am in the process of adding support for various Famicom controllers in the Retro Adapter firmware. I have a trackball and a mahjong controller I am working on. I thought it would be easy enough to find the Famicom controller port pinout online, but both of the pages I found (here and here) are wrong.
The correct pinout is:
1 - GND 12 - Latch 13 - Data 14 - Clock 15 - 5V
There are some other lines connected to the microphone input, but I didn’t trace them. The controller I have has two PCBs held together with wire links so I could not see the markings on any of the ICs or even where many of the traces went. The controller has autofire which works well, although the two speed settings both seem quite fast. My guess is that they are clocked by the latch line so speed would depend on how fast the game reads the controllers.