It would have to be one hell of a vibration to affect the PCIe connector adversely, especially if your PC has those hooks that are common on PCIe16x sockets that grab hold of the graphics board to hold it down.
I can't vouch for how much your WD drive should or should not vibrate - my own WDs, two 1TB Raptors and one 3TB Green series drive hardly vibrate any, but the Raptors have very low rotating mass (only two wafer-thin 2.5" platters), and the Green is a low-speed unit, so therefore inherently less...vibratory...in nature. The Green you can hardly feel at all when it's spinning, it's kinda creepy really.
I can't vouch for how much your WD drive should or should not vibrate - my own WDs, two 1TB Raptors and one 3TB Green series drive hardly vibrate any, but the Raptors have very low rotating mass (only two wafer-thin 2.5" platters), and the Green is a low-speed unit, so therefore inherently less...vibratory...in nature. The Green you can hardly feel at all when it's spinning, it's kinda creepy really.