I did everything via ssh, then when I was able to get to the machine and turn on the display, it was working and I had access to 4,705 arcade games! True, hundreds of those were just Mahjong or different versions, but all the stuff I had fun playing in arcades is all there.
Thank you for all the help, everyone. I managed to compress my entire collection into CHD files. Much cleaner, and much smaller space-wise. And, they all work...except for the Sega-CD 32x games (there's only three or four of those). I guess I have to do some more homework on that one.
Not all my images were bin/cue. Getting them to be bin/cue so I could convert them to CHD was tedious and sometimes frustrating, but I got it done.
@synack As far as the end user is concerned it works just fine as is. They scrape from SSelph and it gets say 90% for a given system. Then they scrape from the built in scraper (by filtering on roms with no images, the games db, and for the given system). They manually resolve conflicts. Now they may have about 99% of the roms scraped for that system. 90% of the images are in the directory SSelph scraper uses, 9% are in the directory the built in scraper uses, and 1% couldn't be found. So it all works. Me (and my OCD ha) would like it if all the image files were in SSelph's directory. So your options are
leave it as -is and don't worry about it
Manually copy the images over to SSelphs directory, then open up the gamelist in notepad and find and replace
Write a script (or use the script I wrote) to do #2 automatically
In honesty I should have just done #2. I sent more time testing and getting the script to work. If I just manually did it I'd have it done in probably 20 minutes.
I've tested it so far on the virtual boy, the n64, the Sega 32x and the SG1000 system and the script seems to work fine each time. I wish I could get to 100%. The "Add Input" button in emulation station is weird. I can find WWF RAW on thegamesdb.net but I can't seem to type in anything in emulation station to find it. I wish I could just type in the gameid in the "Add Input" button in Emulation Station.