I've not worked on many of these D.E./Sega Sys 3 games but I would think the flipper board has to trigger something in the matrix when the buttons are pushed and the only ones that have anything to do with the flippers are the two EOS ones. You could use a jumper and diode to manually simulate those switches and see if the matrix registers them and if so if the initials/lane change works. Are the flippers even supposed to do any lane changes (i.e. skill shot) on this game, it's been too long since I played it to remember? If it does you know the problem is probably on your SSFB.

BTW - some games with SSFBs do use EOS switches, I know for a fact that JP does and if they aren't working it caused major issues with the flippers.

3-5 go to the switch matrix.