Here is something that helped me get a lot of the arcade cores running:
The scripts are actually pretty great, I plan on keeping the MiSTer hooked up to a network cable at all times. I just have to get the right versions of ROM out there for a few games like Spy Hunter and Tron."Finally realized to run MiSTer executable in shell to see what it was actually doing and discovered it was finding and trying to use old unrelated /media/fat/mame folder instead of /media/fat/_Arcade/mame."