Is there a way to re-oragnize the files back the way they were originally on the computer?
If you mean can you restore the folder structure then yes, if you are in Advanced Mode check Options/Actions Restore Folder Structure. This will build up the folder structure on the drive you are recovering to: you can then copy the file back to the live drive.
Folder names that have been lost - indicated by a ? - are not recoverable.
If you mean restore the file names where they have been replaced by a number and extension, unfortunately not.
The file names do not have "?"s and it seems they have been recovered, though the files cannot be opened. They were recovered from my computer ( which died) to an external back up drive, not sure if that helps.
I made the setting change to keep for folder structure, do I now try to recover the files back onto another drive so that the program organizes the folders?
1) It's folder names, not file names.
2) Yes, although if the files can't be opened it does make the exercise rather pointless.