David, if your images folder structure is intact, and you just missing all your xml files, you could try the following procedure:
1. Take a copy of any good header (xml) file from your good document.
2. Create a DOS batch file that would copy this file to each of the folders that have your pdfs while renaming it with the folder name - If you don't have experience with this, let me know how to contact you. Run the barch file - it should copy your sample xml 3500 times this should allow you to open images in Docuware.
3 (Optional) Run a Docuware Restore Services workflow - Database overwrites document