If the switches are working I would start easy and check the trough for physical issues. It was a very common issue for DE and subsequently Sega troughs to have issues with those switches needing constant adjustment to activate consistently and balls getting physically hung up in the trough and not rolling properly to trigger the switch. I would mess around manually with the coin door open and drain some balls in switch test and watch the behavior in the trough and see if there is anything you notice.