If you are interesting in home-built CPUs then you've got to start at the home-built computers web-ring.  I doesn't have everything, here is my (somewhat ordered) list of favourites:
  1. Megaprocessor   This is fantastic, it has LEDs everywhere and lots of documentation and tutorials on how everything works.    I first thought "Damn, someone has beaten me to it" but my goals are somewhat more modest in size and cost and I'm aiming for reproducability and education - that's a new challenge.
  2. Relay Trainer  I love this one.   A whole CPU in 83 relays, all instructions have the same format and you can see everything at once on one board.
  3. Magic-1   Unbelievably complete, LCCMINIXTCP/IP stack - amazing.   The ISA for Magic-16 is also worth reading.
  4. A dis-integrated 6502 this 6502 in transistors is only 12" by 15" - it shows that it can be done.
  5. AYTABTU (All Your Transistors Are Belong To Us) this one has stalled but it does have a 14T per bit ALU which looks interesting.
  6. 4 bit computer built from discrete transistors it can't run much but it's honest in how hard it was to build.
  7. Harry Porter's Relay Computer Great work, and if relays were much faster and smaller I'd be tempted to use them.
  8. Heath Robinson Rube Goldberg Computer  Not really a computer, but a great collection of ideas for building logic gates and memory.
There are many others, the home-built computers web-ring really is the place to start.  It took me very many years to get on top of all the ideas, but it was fun.

If you are prepared to skip the hardware, then nand2tetris gets you all the way from logic gates through assemblers, VMs and compilers to games.  There is lots of open source software, courses and a book available online.   In fact, this covers so much of what I wanted to cover I've reviewed my goals, if you want education from the logic gate upwards then I recommend this course and book over what I'm doing.