Thank you for the pictures.
The first thing I look at is mechanical problems, but if your plunger was mushroomed you'd feel it when you manually activate the flipper, and from your picture it looks as though you've fairly recently replaced the 'plunger-link-sleeve-and-stop'. (That's one part in my world...)
You use a 520-5033-00 flipper board to run your flippers.
Look inside your coin door when you press the flipper button to make sure the LED's are responding properly to the flipper switches on the side of the cabinet. Weird flickering, or delayed response and I'd first look to the flipper cabinet switches.
These flipper boards have absolute crap fuse holders. Frequently you'll pull a fuse and find it rusted or corroded, and that's not rust or corrosion, it's where the fuse clips have done such a poor job connecting to the fuse that it has arced. Little sparks chewing away at your fuse...
It is quite common to have to replace the fuse clips after removing fuses on these boards, they'll fail as you press the new fuse in place.
Bad fuses, bad fuse connections are one possibility here, so check that first.
Then it's board repair... and these small TYFFASI boards can be difficult to repair. About 50% of the time I'll do some small things and then just buy a replacement flipper board.
Let us know what you find.