stalling screen, silent harddrive? 10.8.4

I recently had a corrupted volume directory on my boot hd. I installed a larger 3T drive and used Techtool Pro to export, clean the directory, and optimize. I ported the fixed clone to the 3T and made it the boot drive. The old boot still says it is corrupt.

HOWEVER, I am noticing a problem that may be related to a hardware issue and I don't know how to tell for sure.

The symptoms are: after a time of inactivity, I come to find the screen unresponsive. The mouse still moves but browsers will not load pages, Mail and other programs become completely unresponsive, and the spinning beachball of death happens when you hover over finder areas. Quitting programs will not quit, nor will force quit work.

The harddrives are silent and hitting keys does not "wake up" the system. It seems like there may be a communication problem with the logic board and the harddrives?

Also, upon restart, it is taking FOREVER to boot. I see the grey screen with the Apple and it is grindingly slow. The harddrives will cylcle up but it seems like it is just taking way too long. This is before you get to the login screen names.

Also, I installed 10.8.4 yesterday, but did a safeboot, fsck, permissions repair, etc. And today I redid fsck and it found 45 orphaned files. That seems like a stall sympton that isn't writing properly to the directory, which often happens when things stall out.

SMART tests pass for all drives which have it. I'm wondering though one drive could be starting to fail and cause a problem.