Why do you need 2 unos?. Can't you just read from the SD card and then output the value?
The second arduino is an Arduino Mega with the Adafruit Touchscreen shield. I don't want anything to interfere with the motor operation to ensure the motor's movements are as accurate as possible. I can't read from an SD card, decode the value into an integer, calculate a motor delay based on that integer, and then step a stepper motor while maintaining a touchscreen display without affecting the motor timing.
I had considered what you spoke of JoeN (11 line bus), but tomhow mentioned a timing issue and he was right. I tried setting up a 4 line bus and found it really hard to keep the two boards in sync. I also need the bus to be bi-directional so I know if the motor struck something, if it was rebooted on its own, if it's even on, or if it's receiving the sent info correctly. I found it really hard to program something like that in a reasonable amount of time. I was hoping something similar was out there, but SPI works great.