That wiki was invaluable to me when I took computer organization courses. My recommendation would be to learn x86 assembly and C (also familiarize yourself with gdb!) by writing programs that run on a Linux system and only after target bare metal programming by using something like QEMU + gdb or Bochs for emulating bare metal hardware that's also debuggable.

(I used x86 assembly as an example assuming you wanted to boot your OS on a PC. An alternative could be to target a well documented SBC like the BeagleBone Black)