Okay, I got it working properly. I ended up downloading a new version of the Ultramap utility (the one I had was in a folder I copied over from the old install, not sure it if matters actually.) Then, with the new utility open, I unplugged the controllers one by one and then searched... they were found. I ended up setting player 1 as ID #2 and player 2 as ID #1. I don't know what happened but it fixed it although having it swapped like that bugs me for some reason. I played a handful of random games that I knew had different button mappings and everything worked out just fine.
FYI the buttons on mine are laid out in a street fighter layout, plus a lower left button kind of like the run button in MK3. So the buttons are mapped with anything 4 buttons or less use the bottom 4 buttons that has a slight curve, and 5 or more use the rest. The second button on the top and the "run" button are actually on the same circuit because I don't know of/play any games that use 7 and this saved me from running out of inputs on the U360s (6 player buttons plus start and coin.) It was a pain to map all the games, I had a program that did it automatically but it missed a whol lot of them so over time I've been picking away at it.
...now I just gotta get the aimtracks working. Another day!