When I was first learning Linux (almost 20 years ago [yikes]), I installed it by hand using the Linux From Scratch guide. It was invaluable for learning a ton about how Linux works at a deep level. While a lot has changed since then (mainly due to UEFI), that knowledge is still valuable for understanding how a system functions.
Gentoo taught me Linux. The Handbooks are really good.
I think that much of early Gentoo ideas - the OpenRC init system, the ports system, the handbooks - were inspired by BSD traditions. OpenBSD and FreeBSD each have good documentation. Working through the FreeBSD handbook, and then study of McKusik's BSD Book [0], are a good way to get another perspective if you get into this sort of thing.
http://linuxfromscratch.org/