I have a few suggestions regarding your schematic:
Thank you so much for taking time to look this over!
- Add a 1K resistor from atmega RESET pin to +5V.
Ok. Are you sure on the 1K?
I've looked for some documentation for this and the recommendation seems to be 10k or 4.7k
- Add a 6-pin ICSP header so that you can reprogram the chip in-situ.
The board has to be reasonably small (without going SMD). I can't find a good place for the 6-pin header and more importantly, I can't find a place where I can run all 6 wires without crossing traces. I will solder in a 28-pin socket, so I can remove the chip for programming.
- Add a capacitor of 220uF or more from the +12V supply near the fan output pins to the emitters of the TIP120s.
The TIPs are controlling CPU fans. I read that these already have the caps built-in. No?
- Very important! Add the recommended input capacitor and (if applicable) output capacitor for the 7805. The capacitor I suggested at point (3) may be able to double up as the input capacitor, see what the regulator datasheet says.
Looks like the 7805 datasheet says 0.33uf. I shall add that.
I haven't checked your PCB layout.
Any input on that would be appreciated.
Thanks again for taking the time to look this over!