Is using an adapter to use the GameCube controller on a Nintendo 64 or wii allowed becquse you're still using orginal hardware just a different controller.

Yes, it's allowed. The rules say

"Remapping controls is allowed, but each button must only be one input (no macros) and no analog to digital conversion (ex. mapping full left on joystick to a button)"

So long as you're not mapping an analog direction to a button, you're good.