Did you look at the wires on the coil? At the flipper switch?

Did you try switch test as advised? Fuses? Check all easy stuff first

It is the KISS method first always, as you may have accidentally pulled off a wire while working.

You guys with those fancy pants pins. Wish I had a flipper problem like that.....staged flippers.
Sounds like a good clue for sure. I am very interested to see if just coincidence of not.

Well do know that you can use any digital camera to see if the transmit part of the opto is outputting light

You can pull the board check header pins.

Is that with the mod rom in??

Now put the original in and retest the switch test and see if results change.

Really clean the opto and switch the flipper board before going off the deep end and swapping mpu boards.

I never suggest new roms to fix a problem. But in this case it sounded like he had a fully working game changed rom had issue. But now that he is using switch test and is seeing that it is not reporting the lower right flipper. Put the original back and see if it still reports the same. It should. Then keep the original rom in and fix.

Yeah trying to help when not familiar with machine is sometimes not good.
Just hoping to spark some basic trouble shooting ideas.
So i am going to sideline this issue.
There should be enough JD owners out there to help.