The Mac Pro uses a CPU diode temperature sensor to determine the CPU temperature. The fan speed is then adjusted based on that temperature reading. Low temperature results in low fan speed, and high temperature results in high fan speed.
If the computer cannot determine the CPU temperature, then to be safe it has to assume the CPU is hot and so runs the fan at full speed. This is what you are experiencing. So we know the Mac is not getting the CPU temperature reading.
Because this is happening with both the new and the original CPU in socket A, there are two possibilities I see:
- You have damaged one or more pins in socket A. This is one of the severe risks when using a lidded processor in a dual-CPU 2009. Closely examine the pins in the socket. If you can, take a high quality macro picture.
- You have managed to incorrectly seat the CPU and heatsink, twice in a row (once with the new CPU, and then again with the original CPU). There are many stories here from people who have made slight adjustments (like 1/4 turn) on one or more heatsink screws, with various strange results like weird fan behavior, some memory slots not working, and even a CPU not working or not. Tweaking the tension on the screws changed the behavior. If you have determined none of the socket's pins are bent from scenario #1, then I'd try adjusting screw tension on the heat sink for CPU A (keeping in mind the following warning).
Warning: Be extremely careful when tightening screws. Over-tightening screws WILL cause damage to the socket in a dual-CPU 2009, especially with lidded processors. One person said it happened even though he was using the washer method.