Royally messed up the Windows Server 2008 R2

Make sure that you have the correct drivers loaded for the mass storage device that you are trying to install to.

The computer was booting off one of those disks you removed, and starting the OS from the Operating System disk (which is apparently a separate disk). This is what happens when someone carelessly installs an OS.

You need to get the BCD on the OS disk and corrected for it's new location. You may be able to boot the Installation Disk and Repair the installation into booting again.

Update - To Fix:

• First a backup: run bcdedit -export C:\bcd.backup, should probably copy this to another computer or thumbdrive.
• Open Drive Management, mount the boot partition (should be 100 or 300 MB) to a drive letter, note the letter.
• mkdir C:\boot
• xcopy /e x:\boot c:\boot (where x: is the drive you just mounted)
• bcdedit -export C:\boot\BCD

• bcdedit -store C:\boot\BCD -enum all
  Note the entry identifier and property of any lines where the second column says partition=x:

  For example:
  

  Windows Boot Loader
  -------------------
  identifier          {current}
  osdevice            partition=x:
  

• For each occurrence noted execute the following; be extremely careful to not screw this up!
  bcdedit -store c:\boot\BCD -set {current} osdevice partition=c:

  Note: change {current} to whatever the identifier of the section was for the property you're changing. Then just follow it with the property and new value. Also note the new c: value instead of x:. Also, the identifiers may/will be GUIDs.

• Once that looks all good, fire up Drive Management again, remove the drive letter from that other drive so it's back the way it was. Mark the C: partition Active.

You should now be able to remove the other disk and boot off the system partition. If this doesn't work you haven't messed up the other disk and can put it back in.

Update 2:
Looks like you've got that other partition mounted as h: already, so ignore that mount and unmount stuff, just jump into the copy, edit, yada yada.