Check the easy stuff first:
You did mods and the flippers stopped working so start by checking:

-All connectors get reconnected? No unplugged connecters hidden tucked behind a board or fallen down?
-Check all connectors you touched and make sure they are plugged in correctly, not offset 1 pin.
-All fuses OK?

-In test "T.1" switch test mode, do you see the left and right flipper buttons activate when pressed?
-In test "T.12" flipper test mode you can select R.flipper power and R.flipper hold, etc. Do the flippers move in each of those 4 tests or what happens?

Post back with test and result. You original post was a little hard to follow.

If they work in test mode but not during play they have power. Did you plug everything back correctly? Or accidently pull a connector or wire from one? I've installed alot of colordmd displays and never had it effect the flippers. (edited, I missed that they worked in the test)

If the flipper work in solenoid test they are getting power and “working”. You are having a switch problem it sounds like. When your working with the colordmd your right by the switch connectors on the mpu. Bottom left corner of the backbox. Take a look there and see if when you were doing the Z connector you didn’t pull either the connector or a wire out of the connector on the mpu

Your posts are still unclear. Your saying the flippers work in that mode?

Do they or don't the buttons show being pressed in the switch test mode?

Both flipper optos and the color DMD use 12 volt unregulated, so that's why your flippers only work in test mode. F116 should be a 3 amp slow blow. The color DMD draws about 600 ma, so it is a significant load, but unless you have other 12v based mods, it should be ok. I would re-check the wiring from J117, J116, and J118. You could unplug all, then plug one in at a time until the fuse blows. Then you can tell which line has the problem. Note that J116, J117, and J118 are all interchangeable. They all deliver 5 and 12 volts to various things that use it, like optos, motors, remote boards.

Good, the 12v is stable. It sounds like the power to the flipper buttons is still out. Sometimes the wires break right where they go into the IDC connectors. You're looking at the gray / yellow and black pair. You could also pull on the harnesses to see which one goes to the cabinet and just follow it, looking for breaks. If you have a meter and can measure 12vdc, it gets a lot easier.

The signal path is: 12v(unregulated) feeds the flipper opto led, which when button pressed allows the beam to pass, which excites the other half of the opto assembly to close a dedicated switch input going into the fliptronic board. The dedicated switches run on a different supply (regulated 12v) from the opto supply. Since the flipper OES switches are also dedicated inputs, if you push the flipper bats up by hand while in switch test, it will register even if the unregulated 12v is missing.

Note that if the left-hand flipper opto is disconnected, then neither flipper will work. This is because the 12v is connected through the opto board, so it forms a chain. Goofy design, I know. But it's something to check.

Is it possible that you disconnected one at J118 and forgot to connect it back up? The color dmd has an aux connector on it to replace the space it takes up.

99% sure your problem is one of these connections. I'm going to give the other 1% to the ribbon cable between the CPU and fliptronics board; data along this cable is how the CPU knows if you pressed the flipper button, there are no other connections involved.
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According to your manual,
J 116, J117, and J118 are all used in your game. I see your ColorDMD connection plugged into J116, my question is what happened to the connector you removed from that header?
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Not that ribbon cable, that ones for your solenoid and flasher control, Im concerned about that wire that looks like its pinched under it though.

This is the one I'm talking about:

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LED3 is supposed to be off, just ignore it.

There is a slam tilt switch on the coin door...its probably too sensitive

TP2 and TP3 are test points for measuring your +5V and +12V regulated. You can check them but I suspect if those weren't correct you would have more serious problems

Please reverify you have 12V on the flipper board by checking between the 12V and GND points at the connection point, this voltage cannot be measured to the ground braid.

If this tests good, you will need to do a little more involved testing...do not perform these procedures if you are not comfortable doing so.

With the power off, remove J905 from the fliptronics board.

Turn on the game and put it into switch edge test and leave the coin door open.

On your fliptroics board, use test clips or a wire jumper to connect J905 pin 1 (on the right) to each of the other pins on J905 one at a time (see diagram below for pin locations); each time you make a connection between pin 1 and the other pins on this connector, one of the flipper switches should register a closure. If these switches do not register, you issue is on the Fliptronics board, the ribbon cable, or the CPU board. If these work as expected, your issue is between this point and the flipper switches. The only commonality to all 4 flippers is the orange wire connected to J905-1 and the 12V wire connected to the power driver board.
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Please take a picture of your left flipper assembly inside the cabinet, I just want to make sure I'm not missing something here.

What is you final repair to get it going? I hate seeing unresolved threads.