The power supply fan is a separate module in the MacPro3,1. It is installed directly in-front of the PSU itself, and is removable and listed as a separate component by Apple (fan P/N 076-1294, PSU P/N 661-4677).
Ergo, a faulty fan is most certainly not a faulty PSU, since they are two completely different components. The fan isn't even hooked up to the PSU directly- it runs through the logic board and is throttled by the SMC.
If the fan is defective, it should be replaced. The rotor could be misbalanced or something else could be wrong with it mechanically, which might cause a clicking noise.
The PSU itself does have a relay inside it, but this relay controls the state of the DC output. If the relay were clicking, the entire computer would be turning on and off and generally freaking out, which makes me think that the fan is defective and not the PSU.
You should probably just open the machine up while it's running and listen around to determine where the noise is coming from. There is only one fan in the entire top portion of the system, and that's the fan in-between the optical disk drives and the power supply. The PSU does not have a fan built-in anywhere.
-SC