The best case scenario, yes, empty, though I believe there is a non-destructive version, but I don't know much about if it would take longer for it to function (does it move your existing data around as it tests the places that are occupied?), and there are other things about that method I'm not sure about...

If you're willing to start over, I highly recommend the test. On that note, you might as well start over since a boot drive (be it SSD or a small HDD) would likely be the preferable way to build this encoding system. Nice big data drives that don't have any system files also being accessed, and less danger of accidentally wiping them or screwing up partitioning if you have to reinstall the OS... Also no GPT booting weirdness for you to have to deal with (GPT being the obvious best way to handle the large, non-boot data drives, though).

My recommendation is to play around with the system a bit as is, but get a boot drive and test every hard drive and run a mem test (I can walk you through that, too, it is also on the same LiveCD you'd be using) before any return/replacement policies run out from the place you bought your stuff from.

3TB HDDs, will probably take a day and a half each to test, btw.