@string7th you can put emulation station into kiosk mode and set all the menu options as "hidden" so the retro pie menu doesn't show up. To bring back full menus, you use the konami code. As far as retroarch, open the configs from your network and go to
configs/all/retroarch/autoconfig and open the controller you want to edit. you can just remove the input_enable_hotkey_btn line and that pretty much disables hotkeys for that that controller. If you want to disable all hotkeys except exit, go through the file and remove all the features you dont want like save state and menu toggle, ect.

@megafacehead No worries, whatever you are comfortable with. As for a fresh install there is nobody on this forum who would not recommend doing it. Pre-made images can be full of junk, unknown tweaks, configs and who knows what else... In fact a lot of people probably didn't even bother with trying to help you once the saw you mentioned buying a pre-made image. You can back up the ROMs folder to your PC and then just transfer it back after a clean install. That'll save you some time.