I spent a few hours tonight attempting to diagnose what each wire on the Viper GC is for, and the symptoms of that single wire being not securely connected, or not connected at all. Here is a run down:
Yellow Wire: This wire appears to emit the signal for the Cobra BIOS so that the factory GC BIOS is overridden. If you experience (after installing a Viper GC module) the console booting originals directly (as if pressing X @ bootup with a functioning Viper GC) or as if no Viper GC is present at all then there is a good chance you need to re-check this wire's connection.
Purple Wire: This wire appears to be the harness wire that goes to the GC mainboard telling it the "bypass" state of the lid sensor... it gets it's information from the BLUE wires and bypass plugs hooked up during a Viper GC module installation. If this wire is disconnected, the console will boot to the GC menu, and if you select Play Game it will show a "?" on the screen even if an original GC disc is seated on the drive spindle. However, if you reboot the unit holding down the lid sensor (to replicate what this wire does) then the GC will boot directly into the game disc on the drive spindle as normal.
Black Wire: To many people (excluding Electricians), the BLACK wire usually refers to a GROUND wire, however, when this wire is not attached by itself and the rest of the Viper GC wires are attached to the GC mainboard, then the console will power ON and scan/boot any original GC disc on the drive spindle as if it's authenticating and loading normally but without any audio/video signal on the TV screen. (Yes, I triple-checked my A/V hook-up when this synptom surfaced and it WAS plugged in securely). The exact function of this wire is not yet known, but perhaps the Viper Team will detail it for us in the future.
Red Wire: To many people the RED wire often represents POWER, however, when this wire is not attached by itself and the rest of the Viper GC wires are attached to the GC mainboard there will be NO laser activity at all. The unit will turn on to "G" logo menu, and if you select Play Game it displays a "?" symbol. Furthermore, when the "X" button is pressed on the gamepad (with an original GC game disc on the drive) it displays a "Please Insert A Nintendo GameCube Game" error prompt. The exact function of this wire is not yet known, but perhaps the Viper Team will detail it for us in the future.