GI: there's a connector in the cabinet with four yellow wires - check it to make sure it's ok and not burnt. Reseat it and see what happens.
Mystery wheel: run the mystery wheel test and see if it is registering correctly. If it is, that's all you need to worry about. If the mystery wheel is showing up in switch test it's likely the wheel is positioned where the opto is being tripped - not a problem.
viperrwk