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.
What is your opinion on the RA4M1 mcu? Granted the chip is more expensive than the 328p, but it offers up to 3x the clock speed and a lot more memory. Which would be nice since I like using the oled displays but they are memory hogs. I would like to stay with 5v vcc instead of moving to 3.3v, so I am interested in this chip. I am going to order an uno 4 for testing. Also as a huge bonus, it has a 14 bit adc instead of 10 bit. Which will be nice because another project I am working on I am adding an mcp 3204, which is a 12 bit.