The schematic suggests you are going ahead with a different arduino pro mini than I thought. But I realized you are going for a small footprint, and it looks pretty compact. This is what I will be using so I can modify for ion-sensing. The schematic will still work with it.
arduino-pro-mini-clone-atmega328-5v.jpg

Looks like you learned that the next generation of machinists suck. They forget to hone the valve guides after they are done cutting. I ran across this about 10 yrs ago, and was appalled that someone could not machine a small block chevy cylinder head properly. The worst part is that today's heads are more complex. I wonder how those jobs turned out. blech.