Looking at the switch matrix diagram in the manual, all four trough switches are in the same column, so I would look for a broken or disconnected wire at one of those switches or another in that column.
Do the other switches in the column work? Outhole, tilt, shooter lane, right eos? If none work, then it could also be the connector to the board.
You mention right bottom flipper is burned out? What do you mean? If that EOS switch is disconnected, it could be creating a problem with the other switches in that column, i.e., the trough switches.
