Hi Matty. I'm in a very similar predicament... x 5. My wife has five 27" iMacs at her dental office running Win7 Pro x64 in Boot Camp, all part of the recall, though not all HDs have failed yet (1 has, 2 intermittently failing, we're replacing all 5 HDs). My advantage is that I have extra working partitions to "borrow" from.
I decided on Seagate Discwizard (Acronis TrueImage) because it promised to back up the PC and Boot Camp partitions. (Ha!) Most had multiple unreadable sectors. On restore, I got a DiscWizard warning that it wouldn't boot because it had no EFI partition. And sure enough, no Windows partition at boot with option-key. After dozens of hours of research and trial and error, I bought WinClone, but it was too late for the 2 we'd already replaced HDs in. I did image the remaining 3 Boot Camp partitions with WinClone, but I won't know until after the HD swaps how the restore will go.
I successfully got one restored and working without WinClone using a combination of rEFIt and the steps in this thread: https://discussions.apple.com/thread/4144252?start=0&tstart=0. See solution; that's what I followed. Thank you SO much Christopher Murphy!!!
The one that had the blinking folder icon on power up was stuck at the black screen blinking white cursor stage despite the Bootrec steps, Windows 7 Recovery Startup Repair, running "sfc /scannow /offbootdir=c:\ /offwindir=c:\windows" was unsuccessful at repairing damaged files. Because of the complexity of setting up the dental software from two different vendors (Eaglesoft and Kodak Imaging), I didn't want to do a fresh Windows install. So I restored a working Windows 7 WinCloned partition from another workstation. I used Produkey x64 (the 64-bit Win7 install disk can't run 32 bit apps) to get the Windows and Office keys from the damaged Windows installation, and I will update the Windows and Office product keys to the original keys for this workstation so I don't have a conflict with the source workstation.
One WinClone note: when restoring, it does NOT notify you (or better yet, fix the problem) if your target partition is smaller than the cloned image. My target partition was 0.3 MB smaller, and all it did was show the completely empty progress bar. I found the solution online, resized the partition, and voílà, restoration happened without incident. I did trigger the 3 days to activation mechanism even though I restored to the exact same computer hardware, despite the only hardware differences being a new Seagate HD (same size) and a 1 MB larger Boot Camp partition.