Backup & Restore to fix GPT/MBR error
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.