Thought I'd post one more update before this project gets put on the backburner for awhile. Basically, I got a little carried away, and the BOM/ FAB costs reflect that. The final project would cost me about $250 for a single prototype (BOM is ~$160, FAB is ~$70, plus shipping import ect).
Future work: I'm still pretty interested in this design, so I might redesign the main board with multiple small 2-layer boards containing the different blocks. These "cards" could be plugged into a main board to help reduce the XY footprint of the design. Alternatively, I could try to populate both sides of the board; I avoided this in REV0 due to a bit of a time crunch.
Update: Well I just bought a couple hundred 555's so I guess I'll continue with this project between classes. Next step is to layout some smaller validation boards for the different blocks (MUX, BCD counter, BCD-7Seg Decoder, Flip Flop).