I'm thinking Ribbon Cable... particularly between the Flipper Driver and the CPU, but it could be any connector off by a pin or a row, or (more rare) a ribbon cable with dodgy connectors.

This is a good time to check the voltages on the dot matrix display. A lot of the display power circuitry on the DMD board gets very 'crunchy' (blackened area of the board, solder connections becoming brittle). Bad power to the actual display itself is something I'd check. Hopefully the machine is in 'poor display' mode when you check the voltages because trying to find a problem that isn't happening right when you are testing is very frustrating!

I've had the power to the display be vibration sensitive... you tap the DMD board and the voltages either disappear or drop enough that the display looks like it's failing (dim). Resoldering a bunch of the solder connections in the display power area of the DMD board fixed the vibration sensitive issue for me.

Check J906 on the flipper driver board to make sure it's still plugged in... that's where the EOS switch inputs come in, but I'm with LTG, it's pretty likely that the orange wire that is common to all the EOS switches is broken right at a solder terminal on one of the EOS switches. Tug on the EOS wires to see if one comes loose.

As for a connection between the different issues and the DMD issues... Well, you removed and replaced the ribbon cables which if some connection on the ribbon cable isn't connecting can cause all kinds of messed up signals, (including display issues, though I've never had a 'failed display' (dim) be due to anything but actual display failure (that's not what your display is presenting as) or dodgy power to the display (which IS what your display issues are presenting as). If you've got compromised power to the display that could be intermittent until you get it fixed.

Let us know what you find.