My issue seemed to be centered around the install directory of retropie, for some reason during my first install attempt it installed itself (although it was missing a lot) to the home/root/… directory.
My issues appear to be solely based upon the folder locations being inside of root (which must have been my error)
I reinstalled retropie again after updating the setup script and everything was installed to the correct /home/pi/…. directory.
I could ssh into the pi and access the root folders but was still unable to add roms. Now that the install is in the correct folder I have no problem adding them to the correct folders especially through samba :)
Now I just have to deal with my blank black screen errors!
Thanks for all the support so far :)