If you want to bounce any ideas off someone, let me know. I've done a decent number of custom boards using microcontrollers. Some general suggestions - I'd use something more modern than a 328P. There are AVR devices with better internal peripherals, more flexible and simpler to implement that cost half the price. Not quite sure how you'd establish timing from the sensor signals alone, since they'll always have a fixed relationship relative to each other.
I actually just bought an STM32 Nucleo to start tinkering with it. But I will probably take you up on your offer as well. As to timing, I was going to start with just getting sensor angle offset from 120*, I hadn't quite worked out what to use as a fixed reference to compare that to.