Success: moving bootcamp partition to an external drive

Background
Due to the relatively small, non-exchangable SSD on my Mac, I'd limited the bootcamp partition to 50GB when installing Windows. I needed to install new software in Windows, but was running out of space fast and didn't have the necessary space on the Windows side. I don't use Windows that often and for that reason, I wanted to move the Bootcamp partition to an external hard drive, freeing up space for the Mac side on the internal SSD. I'd read many conflicting reports on the web, some claiming they'd done it successfully, while others said it would be impossible, because Windows 7 wouldn't run from an external drive. I had a HDD in a USB 3 enclosure, and first tried to install Windows to this (using various guides on the web). I was very close to success with this USB 3 drive, but Windows would fail during start-up. Most reports claiming to have successfully been able to run Windows 7 from an external drive, had used Thunderbolt drives, so I decided to get myself a Lacie Rugged USB 3/Thunderbolt series Solid State Drive.
Hardware used
MacBook Pro 15" Retina Display (mid 2012), 2,3 GHz Intel Core i7, 8GB RAM, 250GB SSD
Lacie Rugged USB 3/Thunderbolt series, 120GB Solid State Drive
Software used
Mac OS X Mavericks, 10.9.2
Windows 7 Ultimate
Plus several free downloads from the internet, see description below.
Procedure
Step 1: Get the Thunderbolt drive to work under your Bootcamp Windows 7 installation.
This should be simple enough, but proved to be a little tricky. Here’s what I did (assumes you are running Mac OS X before you begin):
1. Make sure your Thunderbolt drive is disconnected before proceeding.
2. Restart your Mac and hold down the option key (alt key on some keyboards) during startup.
3. Choose the Windows drive to start up Windows 7 on your Bootcamp partition.
4. After log in to Windows 7, download the necessary driver software for your Thunderbolt drive (find it at the manufacturer’s homepage of your Thunderbolt drive - in my case lacie.com).
5. If the downloaded driver installer is in a compressed format (like zip for example) be sure to decompress it before running the driver installer.
6. Shut down your computer.
7. Connect your Thunderbolt drive to your computer.
8. Start up in Windows 7 (see items 2 & 3 above) and if it all went well, you should now be able to see your Thunderbolt drive under Start>Computer.
Step 2: Format your Thunderbolt drive in NTFS-format.
Still running Windows 7 with your Thunderbolt drive connected and visible to the system, it is now time to format your external Thunderbolt drive in NTFS-format. There are several ways of doing this. I used the procedure described here at tedhhack.co.uk.
Step 3: Follow the directions at intowindows.com to clean install Windows 7 onto your external Thunderbolt drive.
As described at intowindows.com, this involves downloading Windows Automated Installation Kit (WAIK) and running command line tools. At step 9 in the described process at intowindows.com, at the point where the installer asks if the drive you are installing to is a USB hard disk, the correct input is Y for yes, even if your external drive is a Thunderbolt drive (and obviously not a USB hard disk).
At step 10 in the described process at intowindows.com (Reboot your PC), remember to hold down the option (or alt) key at every restart in the installation process, so as not to start up in Mac OS X. Also, since your machine now has two Windows 7 installations, Windows Boot Manager will appear and ask you to “Choose an operating system to start” and there is a list of two Windows.
I don’t know how to tell which one is on the external drive and which one is on the internal drive at this point, but I started with the top one on the list and this turned out to be the one I wanted (the newly installed one on the external drive). If you pick the wrong one (on the internal drive) at first, simply restart the computer and choose the other one. You know you got the right one when the installation process continues and asks for further input.
After the Windows installation is complete (there will be at least one other restart required - remember to hold down the option (alt) key to start up in Windows, and choose the same Windows on the list in the Windows Boot Manager), you’ll be running a freshly installed, but crippled Windows 7, as you still haven’t installed the specific drivers for your hardware. But don’t worry, that will be fixed in the next step.
Step 4: Clone your Bootcamp partition from your internal drive to the external Thunderbolt drive.
In this step you will copy all the software, drivers, settings and other files from your Bootcamp partition on your internal drive to your external Thunderbolt drive. The easiest way to do that is to clone your Windows partition - and to that end you’ll need to download some free software: AOMEI Backupper Standard 2.0 fits the bill perfectly, as it will let you clone at the same time as resizing the partition to fit your external Thunderbolt drive (I went from a 50GB internal Bootcamp partition to a 120GB external Thunderbolt SSD).
1. Download  AOMEI Backupper Standard 2.0 (I used the 17MB download for Windows 7), install it, and run it.
2. In the left column choose “Clone” and in the right column choose “Partition Clone”. By choosing Partition Clone instead of Disk clone, you won’t ruin the newly created (but invisible) boot partition on the external Thunderbolt drive.
3. Press Next and choose your internal Bootcamp partition as the Source Disk.
4. Press Next again and choose your external Thunderbolt drive (your newly installed Windows 7) as the Destination Disk.
5. Press Next again and you’ll get a warning that you will erase the contents of the destination partition and it asks if this is what you really want to do. Press Yes to this question.
6. Next screen is an Operation Summery. Toward the bottom of the Operation Summery screen there are a few interesting options: Edit Size of Partition, Clone Sector by Sector and Align Partition to Optimize for SSD.
7. If your destination partition is larger than your source destination like mine was, press Edit Size of Partition. This will take you to another screen, where you can drag to resize the partition. I dragged this all the way to the right to give Windows 7 the full size of my external Thunderbolt drive.
8. Leave the checkbox Clone Sector by Sector unchecked.
9. If your external Thunderbolt drive is an SSD, put a check in the checkbox entitled Align Partition to Optimize for SSD.
10. Now press the Start Clone button.
11. When the cloning process is done, exit AOMEI Backupper and restart your computer (holding down the option or alt key) to start up in your new clone of your old Windows 7 with all the same software, drivers, settings and files.
Step 5: Enjoy running all your Windows 7 applications from your external Thunderbolt drive!
Step 6: Here is where I need help/advice – can I remove the Bootcamp partition on my internal drive now?
I am reluctant to entirely remove the Bootcamp partition from my internal drive, as I am unsure whether this will disable me from starting up in Windows. I would love to hear from anyone here with insight on the matter.

Step 6: Here is where I need help/advice – can I remove the Bootcamp partition on my internal drive now?
To answer my own question in Step 6 above, no, or at least I haven't found a way yet...
Here's what I've done so far:
Used the Bootcamp Assistant to remove the bootcamp partition on my internal drive.
Booted the system with the option (alt) key pressed down and now there was NO Windows drive to choose.
Therefore I used the Bootcamp Assistant to install Windows back onto my internal drive (including installing Bootcamp drivers in the Windows environment). This time I chose the minimum partition of 20GB for the Windows installation on the internal drive.
Booted into the new Windows on the internal drive and installed the drivers for my Thunderbolt drive.
Restarted with the option (alt) key pressed down, chose the Windows drive, but Windows Boot Manager still didn't pop up to allow me to choose the Windows installation on the external Thunderbolt drive.
Booted from the Windows DVD and chose Repair.
Restarted with the option (alt) key pressed down, chose the Windows drive, and now Windows Boot Manager finally popped up, which allowed me to choose the Windows installation on the external Thunderbolt drive again, phew!
So, I can run Windows 7 from the external Thunderbolt drive, but I have to use 20GB of my internal drive for a Windows installation I'll never use. Not the best solution, but at least I've saved 30GB of space compared to my previous Bootcamp partition - and I now have enough space to install the Windows 7 software I need on the external Thunderbolt drive...

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