I've had this thought for a while, but I'm not sure what to call this exactly. So here's what I want to do: Install Windows 7 on a different hard disk (not partition with a current install on the same hard disk). Remove access to the other hard disks from the new Windows 7 (like a shadow drive). So it has no access to read/write to them. Thinking of doing this by just unsigning drive letters to the "shadowed" Windows 7, but I'm not sure if that will affect the original Windows 7 (to my knowledge the system drive is set by default from the BIOS boot order). Just don't want to risk it just for an experiment. I may have answered my own question here but I'm just wanting some verification. Virtual machine isn't an option, I need full hardware support.
Yes you have indeed answered your own question. If you unassign the drive letter in one Windows installation it will have no affect in the other Windows. In fact both Windows installations will have their respective drives listed as C: and the other one as D: or whatever the next free letter is. If you want to be safe you can always make a backup of your current Windows installation with a program like Paragon Backup & Recovery.
Set permissions for all / whatever users in that windows installation, if you really don't want people accessing them.
Another thing to try would be to sandbox yourself using VMs, but I assume you need bare-metal performance.
If it's for security reasons you should install a power switch for each hdd and switch the other one off before booting.