i have a 4p cp, and i opted not to put in a dedicated 4 way. i know you may not want to build another cab, but if you are building a 4 player panel, why use it for 4way controlled games? build a dedicated classics cab if you are wanting to play pacman, frogger, etc. just my opinion, but thats what i plan on doing.
anyway, for the trackball situation, i got rid of the mouse buttons on my cp and i just use player 1's first couple of buttons for mouse buttons. for the frontend buttons at the top, i just used two, pause and escape. the save and load features are cool, but how many time will you use those? i found that i only used those in certain games in rare occasions, so i just keep my keyboard handy for that.