I'm still curious however-- if you have any insight into how to a) edit files from an ssh gui or b) access putty with my pi login, I would be very interested. I can only seem to do these things via the root login and would like to not have to run into these kinds of issues again.
If you use Putty, you can edit the files via nano. Most of the configuration files are also available via file shares (under \\retropie\configs), so you can use a decent text editor from your PC (Notepad++/TextEdit) to edit the files. None of them require the usage of the root account for editing.