Hi Scott, you could still have a fault with the supply wires to the speed controller. Checking with a multimeter can sometimes still show 12V but it dies when under load.
Disconnect both the input plug and the output plug from the speed controller. Then carefully use some short bits of wire to link the positive supply over to the positive output, and do the same with the negative. In effect you are just removing the speed controller from the circuit. The Fan should now run at full speed just as it did when you used the crocodile (alligator if you're American 🤣) clips on to the battery. Using this method will prove the supply is working correctly.
After that you are looking at either your replacement speed controller is faulty. Or the PWM signal from the PCM is not correct, but you will need to check that with a scope.