Recover GoodReader data after iOS 7 upgrade?

Today I upgraded to iOS 7. I did a backup to my computer (Windows 7) using iTunes first. Later when I restored the backup to the phone, I found all apps were gone. I then went and downloaded GoodReader (once again). I expected the GoodReader app's data to be back after the reinstallation but it didn't.

I also updated iTunes after the upgrade to iOS 7. I tried an app called Dr. Fone but that only gives me photos, contacts, etc. How can I get back my GoodReader data?

This is not exactly answering to my own questions. But for those who knows programming, there is a way to get away with it. For me, I wanted to restore all photos I put in my GoodReader.

I get into the backup directory. Used the bash command:

ls * | xargs file {} | grep image\ data > /Desktop/backup.txt

to list all files and it was printed like this (the first few rows):

2:0006c6f73a741907373e2eabcb3763bebf17bdc8: PNG image data, 25 x 15, 8-bit/color RGBA, non-interlaced
3:000bb4a992491782ef65642e1298244242883c66: JPEG image data, EXIF standard 2.21
4:001c384e486a787bb376cee192ee763858e00274: JPEG image data, EXIF standard 2.21

Then I am using Python to rename those files back to Jpeg or PNG files. There are not the same names as they were originally but this has been good enough. There is a Manifest.mbdb file in the same backup directory. I didn't have much time digging into it but this file looks like to contain information which one can use to restore all information.