KevinArduino:
I can post more of the code if it seems like it is relevant but I feel like the problem is here. When I run this and watch the serial monitor the only thing that appears is "Co" from the serial print command for "Code has started". If I put a delay right after the Serial print it will finish but somewhere else in the setup its getting lost. The code never moves on to loop(). I'm somewhat confident with the basics of code but in this situation I really have no clue where to look. Any ideas?
Please do post the ENTIRE code, or at the very least, a complete sketch that illustrates the problem.
Of course it's relevant. A Serial.begin() and a Serial.println() are not going to fail without something else having first caused a problem. For instance, we have no way of telling what pins your GameCube is connected to.
A schematic would likely help too.