I got the PCBs back from manufacturing and the boards are working well. The circuit is identical to the prototype so I didn't expect too many issues.

I did make an update to the Arduino code to allow I2C peripheral passthrough. The 6502 can access I2C devices using a simple memory-mapped I/O register scheme. I tested this functionality with an RTC breakout board.

I'm considering this project to be complete for now. There's a hundred directions I could go with expansion, but I think I got what I wanted out of it. 

I've included the schematic PDF and the Gerber files for the PCB if you're interested in making a VR65C02 yourself. The Github repo should contain all the documentation required to set up the software.

https://github.com/crmaykish/VR65C02