Beginner Question, Red Wire 12 Volt Output, unsure if it's the correct wire.
Yellow is 12V, red is 5V, black is the nominal 0V. On your 12V fan, red is going to be +12V, so yes, connect yellow Molex to red fan. And black to black.

Connecting red to red will produce the fan running very slowly on 5V, or not at all if that's too low a voltage to get the fan rotating.