Hmm... I had a Spring Break and definitely miss it. Have you had the apron off so you can check the ball trough area out? I know that particular trough area is a bit different in the way it stages the next ball that's to come out during play. Somehow my apron was just not lined up perfectly and it was causing all kinds of issues with the balls coming out. I had to add a small shim under one of the clips the apron slipped into on the right side of the apron next to the launcher area. You'll be able to test the ball trough area and inspect the switches and what's going on with the apron off.
That doesn't explain the flipper issue though.
Is it also possible that the flippers and the trough coils that move the ball into the launcher are on the same circuit? And maybe it's a fuse that looks good but maybe it actually needs pulled out and tested because they don't always appear blown when they sometimes are.
Hopefully if nothing else, my bump helps get your post viewed by someone who is more knowledgeable and able to assist.