I don't think windows 8 has anything to do with why the drives do not show. They should still show up as bare drives in the bios. And if they don't and they have power and good sata cables and have been placed on two different boards..... Something is probably wrong with the pcb boards on them. 
 
Question...were these drives connected to the x58 when it crashed?

No, They were only connected to the X99 Classified, But after I couldn't get them working again on it, Then I tried them on the X58 with no luck.
 
BTW, The X58 Still had two mechanical SATA Hard Drives running Windows 7 64 for Years that still worked, until of course the X58 MB Failed today.
 
I Just don't believe it, But Looks Like for whatever reason all three of the drives that were running Windows 8.1 64 Died.

Can you physically hear the drives spinning?

No, I cannot hear the drives spinning or making any vibrations, But after sleeping on it I think I now know what has happened to these hard drives.
 
Looking back now that I have had some time to think about it, When I was having all the BIOS problems with the X99 Classified (and all Five of my hard drives with Windows 7 and 8.1 were still working), I decided to buy another less expensive Brand X99 4-Way SLI Motherboard for BIOS testing purposes in which unfortunately I found out after assembling it connecting ONLY the two Windows 8.1 drives and another already formatted drive I was going to reload a fresh copy of Windows 8.1 onto, That MB immediately had a problem where it would try briefly to start up when turned on and Then quickly Shut Down my PSU/System.
 
I then tried a Few times more to start the System up and encountered the same problem. Briefly attempted to start, Then shut down the PSU again. 
 
I do remember the other two SSD Drives with Windows 7 64 were NOT connected to this New MB, So that is the reason they didn't fail and are still operating with no problems.
 
I Now believe Since I Only had those three mechanical SATA Hard drives connected (two with Windows 8.1 64 installed and the other one just formatted) to that System when it Failed to start up and shut off the PSU that a Voltage surge/spike caused by the defective New MB may have shorted out those Hard Drives.

Then that would make perfect sense then. I knew I was not losing my touch.

That's rough, hopefully they are under warranty still.

johnksss
Then that would make perfect sense then. I knew I was not losing my touch.

No, You aren't losing your touch John.
It was just me having to sort out and go over again in my mind what happened to the drives during all the X99 Classified BIOS problems along with my X58 Motherboard Failure plus having the other X99 Motherboard I got for Troubleshooting Fail immediately. 
 
I Just had Too many problems going on at the same time.  

EVGATech_DaveB
That's rough, hopefully they are under warranty still.

The Motherboard is under warranty, But I have doubts that the two 1TB Seagate Barracuda's and the 320GB Toshiba are under warranty still.
 
 

Yep, After further inspection I can see it all now.............Had a Voltage Spike that Burnt a few Power connector components on the Hard Drives!
 

Hopefully with all the problems behind me now, Here are a Few Benches using the Stock Factory Settings on both the 5960X at 3.3Ghz and the GTX 980 SC's in 4-Way SLI.