Only few keys working on dactyl manuform

It's very hard to diagnose from these photos, but one question I have is if D, F and space have anything in common? Are they on the same wiring row? Or maybe they all have different rows/columns? Are they all on the same hand? Are the other keys nonresponsive entirely?

Starting with why those three are working might point you to a solution.

Also perhaps look at the diodes - are those three diodes oriented differently to the rest of the diodes? I can't see all the diodes because some are hidden behind wires.

Also without knowing exactly how it's supposed to be wired it's hard to understand what it's meant to look like. What wiring diagram are you going by?

It looks like you've got on the first picture white, orange, red, yellow for the rows, and green white black blue green purple for the columns. There are other wires I can't locate, but it doesn't on the surface look wrong. You could check each connection with a multimeter to ensure there aren't any breaks. If you want to check with the diodes in place make sure you test them in both polarities because multimeters use a polarised charge to check for continuity/resistance. Testing them in one direction should give a high resistance and in the other should give a low resistance.

It's also possible you have a problem with the chip itself. If you have a spare that you can swap out that could be worth trying. I usually have spares because they're quite cheap.

does both sides fail? I would say it's something with your wiring.

Try swapping the cables, also you can do a short in each key socket to simulate a key press but removing the possibility of a bad switch. And check again if all the cables are connected were they are supposed to be

Ahh, the wonderful world of troubleshooting! I would first check the micro controller. Unplug all the matrix wires from it. Plug it n and use a paperclip or metal tweezers to short each of the i/o pins assigned to the matrix (rows to columns) to generate key presses. If it generates all the proper key presses, then it's not the controller. If some are missing, then try again to rule out user error, is still no go, then it's either the controller is bad, or your firmware is bad. Check to see the firmware looks good to rule out which. Next check your diodes, makes sure they are all oriented in the same direction. If not, then it time to de-solder and fix. You can also check to see if there are any broken solder joints in your wiring, fixing any that look broken. If they are then you can carefully reattach your wires, double checking that you're putting therm where they're supposed to go. Then plug in and use the tweezer method on the hotswap sockets. If that works, then test the keys, sometimes the pins on the switches bend, instead of going into the socket. Pull the switch, and straighten the pin (or replace switch) I hope you find the issue and get your board up and running.