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Sounds like what I've been doing manually for a while now as I learn more. For my desktop I have three scripts. One to install Alpine on full disk encryption. One for the initial setup up to the first required reboot and the last for the remaining setup plus transferring files.
I've been learning how to edit files with sed, cat, echo and tee commands to help automate everything from a fresh install.
Similar process for my Pi's except I just copy-paste blocks of commands through a terminal instead of a script.
To transfer files to all their proper directories, I have a whole system for that using rsync. I basically keep a bare-bones directory tree with only the files I have worked on. Then I have an rsync command to send all those files onto the Pi's file system in a way that retains all the files and folder's attributes.
I wrote an rsync tool for myself to help me keep all these commands in files that I can neatly organize. I use that tool so much that it's now my entire backup system. With a bunch of files organized with numbers, I can automate the backup of my phone, two pi's and laptop to a partition on my laptop, then an additional copy to my external SSD in one command. And I have very high confidence in my restores since I do that frequently while testing new stuff. I also failed a lot before to get that much confidence.
I have issues with over organization if you couldn't tell by now hahaha.