Windows 7: Problems recovering certain types of files

I'm trying to recover a range of files in whole folders that were deleted from a healthy drive through Windows 7's Recycle Bin. The drive hasn't been written to since the deletion, so I though it should be fairly straightforward.

I've tried recovering the data (about 900GB !!!) - to a different drive, using the option to restore the original folder structure, but that doesn't work - I get a whole lot of folders all at the same level of the tree, with no reflection of the original hierarchical structure. Thousands of them. They're all going to have to be sorted out manually. And to make things very difficult, the folders have all been renamed with eight-digit alphanumeric strings starting with "$". So the "restore the original structure" option doesn't work.

I've tried the restore on two separate runs, once with Recover My Files and once with Recuva. I get the same results each time - is there something I'm doing wrong?

Also, I notice in the configuration options of both of these applications, neither epub nor PDF are listed as formats to explicitly search for or recognise. So I was not surprised - disappointed, annoyed, but not surprised - to find that all of the recovered epub and PDF files, or all I've so far examined, are corrupt; they have their name, they show up as being their expected size, but when I open the epubs in either Adobe Digital Editions or Sigil, or the pdfs in Acrobat Pro, they're empty. Do the recovery apps really have to know these files and their formats to be able to recover them successfully, or does this mean something else is going on?

One other issue: all my jpgs are similarly broken. This is perplexing.

Can anyone offer any suggestions? I've never had to do a file recovery before (no, really!), so I could just be doing something wrong through inexperience. But I really expected a far better success rate, on what should effectively be a straightforward undelete.

Help!! :-)