Backup & Restore to fix GPT/MBR error Problem:

I had previously had dual booted my MacBook Pro (13" Mid 2010) with OS X 10.8.5 (Encrypted) &amp; Windows 7 x64 with a separate FAT32 partition which I was going to install Kali Linux on.  While under Win 7 however I quickly started running out of space for what I needed to do, as a quick solution I decided I would just merge my Kali partition with Win 7 to create more space.  Despite the fact that I had read before that resizing a Win 7 bootcamp partition was difficult and should not be done I proceeded (without thinking) to do so.  Upon reboot however I encountered the expected,


  Error: No such partition.
  Entering rescue mode
  Grub Rescue >


Luckily I am able to still boot into OS X by holding down the "Option" key on boot.  I have fixed this problem before by manually fixing the MBR table using the method described here --> http://jonsview.com/fixing-mbr-tables-on-imac-or-mbp-triple-boot-setups

Unfortunately I have also erased my Windows 7 &amp; Kali partitions as I was going to just start over from scratch using bootcamp and create a bigger windows partition so that guide is not as easy to follow since I only have my OS X partition left.

My Solution &amp; Question:

What I have decided would probably be the easiest course of action would be to backup my OS X partition, do a complete reformat and reinstall from back up.  However I would like to retain my system exactly as is with the two user accounts, all their settings and apps still installed and operational.  I am thinking cloning my partition would probably be the easiest but I am unsure as to how this would work with an encrypted OS X partition and if it would still retain the MBR error.  My current choices of action from what I can tell is:


Cloning the partition
Migration Assistant
Time Machine Backup


If anyone could give me some ideas on which would be the best solution for me it would be greatly appreciated.
In my opinion, Time Machine is the best solution. If you do a full restore from backup, all your configurations are retained. You'll need to enable FileVault after the restore is finished. If you do a nuke-n-pave and a pristine install, migrating profile data, apps and settings invariably misses some stuff, e.g., VPN configurations, automatic wifi connections, current RVM environment, 3rd-party printer drivers, etc.

If you repartition the drive and lose the local recovery partition, internet recovery will be slow; as such, you may wish to download your OS X version from the App Store and use DiskMaker X to create a bootable installation USB or DVD from which to proceed. Note that a local recovery partition is not created unless you do the actual OS installation first, which'll burn a good 30 minutes of your day. After that, you can reboot to the USB and head into the restore process.