I would suggest using your external drive to do a backup of your current server (with as much data as you can fit) at least the primary disk which has your OS and first data partition - use the Dashboard to set that up. Then boot your server from the installation
DVD and do a server restore to the disk you want to use in your new server - I would leave all other disks disconnected during this activity. Be aware that 3TB disks do not fit that well with WHS2011 as it will create a maximum partition of 2TB and, using
the inbuilt Server backup, you will only be able to back up a maximum of 2TB.
Phil P.S. If you find my comment helpful or if it answers your question, please mark it as such.