Transferring OS to a new Hard Disk - Recovery and Boot partitions...

I had a problem recently with Drive 0.  So I installed Server 2012 R2 onto a brand new Hard disk - the install format / partitioning labelled this new disk as "J:" and it then installed the OS fine to the new drive.  The system however now boots and allows me to choose to boot either the older (C:) 2008 R2 OS, or (F:) 2012 R2 OS.  

So, I really want to remove the C: drive altogether and have the system just boot into 2012 R2.  How do I go about this?  I used disk manager to set the J: OS partition to "Active", but when I remove the C: Drive 0, (which also has the boot and recovery partitions) the system does not boot at all - it reports that boot BCD is missing and fails to boot.

Is there a way to move / create the boot files onto the new hard disk? so that I can remove drive 0

Also, is there a way to create a new RECOVERY partition for the new disk (2012 R2)?

Finally, I noticed when I currently backup the "SYSTEM", using Microsoft Backup, it does NOT create a backup of the system state.  Why is that?  Isn't the system state when booting J: going to be on the J: drive?  I am worried that this backup will not be useful in a case of needing to re-install from bare metal.

Help me please...