Hey djdeck, sounds like an interesting project. I'll try to help out with what I can here. The EV3 and the Arduino are talking over I2C.
First, it helps if you have a logic analyzer available (or an advanced oscope). This should tell you if the clock is running, and if you have your wires crossed (literally the biggest problem if you're working with I2C).
Also, I would double check you don't have your wires (SDA/SCL) crossed between the Arduino and the EV3.
Do you have a picture of the circuit and how you have it setup right now?