@sleve_mcdichael Well, it took awhile. But I did as you suggtested and wrote it using the retropie buster that you linked, reinstalled everything as before. The stephen selph wont install anymore, keeps popping an error. But I was able to use the built in one (Not the one in the main interface but the one through the alternate packages section) and it worked this time!
Thank you!

I was having a similar issue to you and i converted my files to PBP files. It saved a lot of space and made getting images easier (without any duplicates)

@sselph worked great on all of the Systems but the sega Genesis Mega Drive. Thanks again for all your help.