i started with a motion blue build ( romless) and dropped in the roms from one of MLPs 128GB images,
there is some setup to the trackball, which is in the other thread we were talking about trackballs in,
NOW… i did experience an issue where my trackball completely quit working, when i tried installing the aimtrack software,
and i was unable to get it back working again, until i wiped my drive, and started back from scratch,
so… that may be your option there, im not quite smart enough on the software side of things to identify conflicts, and fix them, so my approach was “it was working before i did xx, so ill undo xx lol”
even after uninstallig the aimtrak software for the light guns, the track ball didnt work, hence me going back and rebuilding the image.
sorry im not able to offer you a ton of insight here, but maybe try what i did. install motion blue, then strip the roms from MLPs build and copy/paste them over to the roms folder of MB and see how you fare.