The Color DMD can and will put noise on the 12 VDC unregulated supply about 150 mv. Not enough to cause problems but it doesn't help either.
This is the same rail the Opto's run on.

Did the Flipper Coil you replace have new diodes?

As for the Flipper I'd pay attention to J104 on the Driver Board J901, J902, J907 on the Fliptronics Board.
I bet you anything one of these connectors and or wiring is bad

Check the Voltage at TP 1 on the Driver Board, make sure you have no more than 300 MV AC. Check the Voltage is above 12 VDC.
A bad 15,000 uf cap C30 is worth replacing if you have plenty of AC on that rail