Reinstalling with luks, while keeping most stuff?

I would like to reinstall manjaro, but this time with encryption. There’s an old windows partition I need to get rid of as well so I can use the full drive for linux.

But I don’t want to loose all of my settings and tweaks that I’ve made over the months, but it seems like linux stores config files in all sorts of directories and I’m afraid of missing some.

Have any of you ever done this before? What were your experiences?

the vast majority of your settings is saved in /home
So if you backup your homefolder and restore it to your new install, most things should be there.
Personally i use Back in Time for that.
Maybe also create a list of installed packaged/AUR-Packages so that you can re-install them (easiest would be to use pacman -Qe > installed_pkgs.txt and pacman -Qm > aur_pkgs.txt )