You drive has had a lot of things happen to it! It is hard to know exactly what changes have been made.
First, make sure you have the latest version of Recover My Files, which you can download here:
http://www.recovermyfiles.com, or as you already have it installed, click on the UPDATE button on the main program screen.
I would start by running a Fast Format Recover on the physical drive - this search should take less than 1 hour and you files will be displayed in Folder View of the results screen.
The next search you should try is a Complete Format Recover. Again search the physical drive, and search ONLY for the default selected files types, .doc, .xls, .ppt, .avi, .bmp, .jpeg, .pdf, .wav. All files will be located (not just these) and displayed in Folder View at the end of the search.
If you still find that you are missing files, then try a Complete File Search of the physical drive searching for specific file types.