ai03 has a great set of articles explaining the 101 of making a keyboard pcb amn using KiCad. I started designing my own PCB a couple weeks ago and it was very helpful.

Understanding or knowning what components to use and why they have the value they have is the challenging part for me. Sometimes it's detailed in the documentation of the integrated circuit, but sometimes you just have to look for what others on internet did.

coseyfannitutti did such a great job with those designs and was so kind to leave them all open source.

I recently built a self sourced discipline, and just like you, the flashing of the blank MCU was the more nerve wracking part. I followed this guide with a spare esp8266 I had laying around. Then I had some ArduinoIDE example of an AVRISP over wifi flashed on the esp. Very janky to use avrdude remotely over wifi to flash a blank mcu, but hey, I managed not to brick it.

Dunno if you used flux when soldering your usb-c socket but it helped me tremendously. I bought one of those syringes of thick flux and it made it quite easy.

Also one thing I noticed from the BOM list is that some components were unavailable but only because of the packaging they come in. Some parts come loose and some come on tape (most likely to be use in pick and place machines). On Mouser for example, the same parts in different format have a separate part number. In my case, one of the part was unavailable in the tape form but available as loose parts. So it might be that you dont have to look for an alternate manufacturer, but the same exact part just in a different packaging.

Grats on the build.