If the mega32u4 on the Uno is sending the bits over at 0 - 5 volts will it screw up the mega on the target board given that Vcc will be 3.3V?
Yes. The 5vdc signals (clock and data out) will cause the input protection diodes to conduct on the 3.3vdc powered target chip. So means must be taken to limit the voltage of the control signals to the same as the Vcc voltage of the target chip, via voltage divider resistors or voltage translation IC, etc.
I ended up just throwing a 10K resistor on the Rx line of the target board to limit the current going through the input protection diodes when they conduct. It seems to be working....i.e. no dead pins or smoke...yet. I seem to remember reading somewhere that you can do this. Am I wrong, because if I am then I have to rethink another part of my circuit where I have the unregulated LiPo battery voltage going to an ADC pin?