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Zieg, do you still have the parts car and the engine from the new car? I would swap relays and temp sensors if you do. I'm not 100% sure on this: the a/c might be tied into that circuit too.
I have had an air bubble in the cooling system fake out the senders and set a code in a Malibu before. Had to back it up onto and embankment, and run it to get the air completely out of the system. Just a thought.
If you ground the dark green wire at the relay socket (Ckt 335 in the image Vile posted), does the relay 'click' and fan run? If it does - qhm the dark green wire between the relay and the PCM. If not, do you have 12 volts on both red wires (Ckt 542) at the relay socket? Is it safe to assume that when you bypassed the relay, you did so by jumping the relay socket? Flip the relay over and compare the terminal numbers on the relay to the diagram - is the socket wired correctly?