First of All, I must acknowledge MANY Thanks for All the Hard Work at the Staff of EVGA in Solving This particular BIOS Problem!
 
After Consulting last night and being contacted by Jacob who has sent me a Few Special BETA BIOS's to try out, But that have NOT BEEN OFFICIALLY RELEASED Due to ongoing Testing with the Techs at EVGA, I am Happy to report I have found one that works and FINALLY have been able to Enable 4-Way SLI using four EVGA 980 SC's on my EVGA X99 Classified Motherboard!

 
I Do Not know When EVGA will Officially Release this Updated BIOS as of Yet, But I am Sure it will be available soon.
 
Here is a Bench on 3DMark Fire Strike Extreme using 4-Way SLI with four EVGA GTX 980 SC's on my EVGA X99 Classified at Factory Stock Settings.
 

AWESOME!  Glad to see you are up and going on this, we are finalizing it now, hoping all the checks and balances are done by next week and it is in full release.
 
OK, onto the benching! 
Now I'm torn on appropriate benching music for the current situation.  Either AC/DC Back in Black, or Aerosmith's Back in the Saddle.
 
And to the community, we aren't perfect, and don't claim to be, but I will always do everything in my power to get these things fixed, and I assure all of you, your complaints are NOT falling on deaf ears.

Rudster816
For the right price I might be interested...

I am certain you would put it to good use.  I am surprised you don't have one already.

OK, First Problem:
So I got the X99 Classified to run 4-way GTX 980 SC SLI on Windows 7 64, But Now I have a problem trying to re-install Windows 8.1 64 on Three hard drives that formerly had Windows 8.1 64 already on them.
Now it seems that when I try to install 8.1 using my same 8.1 disk, it WON"T recognize any of the three Hard Drives that had it originally installed on.
 
Second Problem:
My Original EVGA X58 3-Way SLI Classified that I had in use as my Second Computer, DIED this afternoon on me and now I have to replace the Motherboard with either a used one from Ebay or where ever, or turn it in for an RMA to EVGA who undoubtably will have to replace it with an X79 Board that requires a different CPU (2011 instead of my i7-980 1366).
 
That leaves me with only my Old Dell 9100 Inspiron Laptop to use and if IT goes South, You won't be hearing from me very much.
 
Looks like it's going to be quite a while before I can continue with any more tests/benches until I get these NEW problems sorted out!

@Rudster816
I had almost bought that chip as well.
 
@Hallowen
Meaning 3 separate drives or raid using 3 drives?
I can probably help you get it installed though.

When they don't show up on the screen in windows setup means that the driver is not loaded for the drives to be seen.
Is raid enabled in bios and do the drives show up as non-raid drives? Do they show up at all in the boot screen information? 
Have you tried installing using ahci mode?

 Did you break the raid before trying to use them again?

 Try something like Acronis start up disc. If they show up wipe them.

They are all Mechanical SATA Hard Drives with no cracked/missing pins and they were operating fine on Windows 8.1 64 when I was using them separately after I first started running my X99 Classified until I pulled them out of the System to rearrange some components and then when I re-installed them, That is when they would not boot or be recognized.

Yes, I checked the connections and tested them with a Volt/Ohm Meter to make sure they were receiving power at both ends of the PSU cables.
 
It is very Strange that nothing happened to either one of my SSD's that are also on my X99 Classified running Windows 7 64, But All three of my Mechanical Drives running Windows 8.1 64 are not operating or showing up anywhere?

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.

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.

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

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.
 
 

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.