@mitu Thank you for making my pads usable again each time it breaks.

In the latest version of retropie you can set up a specific button as "enable hotkey" button. So you could set a different button for the controller that you are using. Did this for my Genesis controller too.
Other approach would be to set the enable hotkey in the config files only for this emulator to a different button.

@plumpy There's a controller configuration menu in Kodi.

I got it working!! you may close this thread if need be or leave it open for everyone to see if this can help them anyways.....

i feel really dumb but live and learn right anyways so i extracted the iso from the gz file using 7zip which i did not read up on stupid of me anyways i used winflash tool and burned the img on to my sd card and it corresponded took the retropie and finished :)

still does not explain why at first it would not take my sd card when i flashed it and put NOOB on it as i was not burning on to the sd because it states it does not require a burn but anyways :D

@Katemonster It works! I swapped the wires and it works flawlessly now! Thanks for your ongoing help :) I'll edit the top post to reflect the changes.

@faugnom1 I used its default config for two snes controllers so I've never had to mess with it. Maybe it won't get created until you set it up once.

From the RetroPie-Setup I uninstalled unnecessary components -- remove WolfRam, SonicPi, etc. Nothing more than a boot to emulator, so I figured I would get some clutter out of the way.

I then went back to trying to different gamepad configurations through the driver config file. I enabled all four ports and through sheer dumb luck GPIO7 (gamepad4) started reading. I still cannot get GPIO2 / GPIO3 to read the data from the controller, but I have two working NES controllers right now!

I also tweaked the /opt/retroarch/configs/all/retroarch.cfg

There is a setting for joypad input scan cycle -- something along those lines -- that I opted to put at a value of 0 (I am trying to recall this from memory as the NES is now wrapped under the tree for dad) so that it would update controller state on demand. It was defaulted to 2 and the notes in the file were about adjustments for latency issues.

I also had to copy the configuration for player1_input* and update it for player2 within /opt/retroarch/configs/all/retroarch.cfg.

Also removed the override line from /opt/retroarch/configs/nes/retroarch.cfg

Still no idea why I cannot access GPIO3 / GPIO2 -- if anyone has any troubleshooting ideas I would be happy to jump through the hoops. I have the other SD card and another Pi3 at home I can run through.

@gjtorikian your kernel was old.

That video worked fine for me with an original SNES controller. What problem are you having?