Generally digital pin 0 and 1 are used for communication with the host for reprogramming or serial monitor, and generally a bad idea to re-purpose them while testing and debugging. As it may cause interference and prevent the host from uploading new sketch.
Is there a way for the chip to check during "void setup()" section to see if there's something on those 2 pins that may indicate hosts wants to speak? If there's nothing, switch them to output mode and run void loop() as normal. If there's something trying to speak, set them to proper I/O mode and not go on to the loop section of the sketch?
I am testing something on a breadboard to get ATMega328p to run without the shield, and using Uno shield for uploading sketches and I don't want to end up with a chip that has flawed script and won't "listen" for revised script.