It seems I didn't explain that very well.
To resolve this issue and move forward.
I want to create a RAID drive on this board and boot from the shell to the windows PE, create a GPT disk using diskpart then install Windows server 2008 R2 Enterprise so I can use the full 3.726TB.
In the BIOS under mass storage controller configuration it shows the AHCI option ROM.
It states "For AHCI capability in EFI, the AHCI legacy option ROM should be set to [Disabled].
I had this set to "Disabled" and I was able to boot from the shell prompt Fs0: using the following command.
\EFI\BOOT\BOOTX64.EFI
This launched the windows DVD in the optical drive.
What I want to know is can I use diskpart and convert the VD that I created with the Intel MATRIX RAID or using the Silicon 3114 hardware RAID card to a GPT disk so I can then install Windows?
Do I have to set the EFI optimized boot under boot options?
I understand if I set this it disables the onboard RAID wich you have already stated RST is not compatible with UEFI on this board.
Keep in mind I am trying to do this NOT on a single physical drive but on a RAID set VD.
Would it be easier to just partition the VD and forget converting to GPT?
Do these BIOS options only apply to a single physical drive over 2TB and not over a RAID set?