You can use any pins from D0 to D21. You can find out where each pin is by searching for "nicenano pinout". You will have to change the firmware later to fit the chosen pins.

If you already have a Firmware you can find the pins (at least in QMK) in the info.json or config.h file. I have never used ZMK but the used pins have to be in one of the files.

haven't handwired a board yet, but no matter whether it's with pcb or handwired, you'll either need enough pins to direct-connect every single switch (probably not the case) or you'll have to use a diode-matrix. for learning about those, i'd suggest taking a look at this kbd.news article: https://kbd.news/The-Japanese-duplex-matrix-1391.html

for a general handwiring guide, check out Joe Scotto's stuff, e.g. https://www.youtube.com/watch?v=hjml-K-pV4E

I made mine this year, but used pro micros instead of the nice nanos. Used a perf board to attach the controller and TRS connector. Zip ties to attach the perfboard to the case.

Hey, in the bastardkb docs, there is a tray holder for the nano/pro micro that looks to fit inside your build, also works on my Scylla. It's its own repo. I think you can slip the battery between the pins.

Then check if your are rol2col or col2row, there is explainer inside the zmk docs.

Next, find the pins, n!n pinout, and make sure your overlay and dtsii? File has the right order of matrix,. eg the 0,0 0,1... 0,5 and that it matches with how you wired your board. And the right row2col setting.

Zmk docs also has a nice explainer for he matrix stuff.