Make sure SMART is turned on in the BIOS for your HDDs. That'll warn you of imminent problems.
Go to the website of the HDD maker. They'll probably have a downloadable diagnostic utility you can run against their disks, which will reassure you that the HDD has no problems.
Try putting it in a different bay if you're getting a vibration in that one. (Swap the 2 HDDS from bay to bay if you don't have an extra spare.)