johnksss
 
@Hallowen
Meaning 3 separate drives or raid using 3 drives?
I can probably help you get it installed though.

I have Two separate drives that originally worked with Windows 8.1 64 on my X99 Classified, and One Drive that worked with 8.1 64 on my X58 3-Way SLI Classified that I can no longer install ANY Windows on them due to they do not show up on the Windows install Disk screen?
 
 

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?

Very true, if you have RAID enabled it may be the issue, and you would need the driver disk for that, or download the drivers and put them on a thumb drive.

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

I never had any of them in RAID, They were all single drives.
 
They don't show up when connected to my X99 Classified OR my Old X58 Classified, Plus it doesn't matter WHICH OS I try to load (XP Pro / Windows Vista / Windows 7 / Windows 8.1), They have not shown up in the installation screen ever since I first installed Windows 8.1 64 on them and then removed the drives. 

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

They don't "have" to be in raid, only have the raid driver to see them. Just like the need the achi driver to see them. The only one that does not need a driver is ide mode.
If they do not show up period....one of two things... the pcb could be bad due to some sort of power surge or the connectors are cracked or missing pins.
 
I would suggest plugging them up to an external usb adapter if you have one. If not...could be the drives are now bad. Are these ssd's by chance?

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.

I know you have done this, but did you check the power cable form the psu to make sure it's plugged all the way in? (psu side)

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?