@tamperedmedia i think I fixed it . Double checked all of my wires and ,while identical, select and start weren't connected in the right spots on the encoder. Once wired correctly I set both bindings in retroarch without bothering to set player 2 on the retro pie home screen. It still inverts up and down for player 2 on the main menu but it seems to work properly in game so it'll work as it is.

Hopefully it won't break again, appreciate the help.

@simotsu I figured it out... After reading this forum a little bit I found that I had it wired incorrectly. So off to the races now!

Thanks so much for you help i am going to take you advise and return and get a core setup.

@dankcushions thanks!

I am using Asciinema for that for some time now.