So have the original backup on your computer? (post initialize) So no matter what changes we make to the drive we can just restore that image.
0) Because of what you said in step 3, do another image of the drive with a HEX editor, I recommend FlexHEX, it will let you open and save the drive as "Physical Drive"
1) Since we have a backup of the drive go ahead and format it in the PS3 (if you got time to waste FULL format in the PC to get all 00's that way the changes are more noticeable by the human eye as well, but that's not necessary)
2) Put that drive back into Windows and then without initializing it, clone it (though that's what I originally wanted to try but the drive just wouldn't appear in any program till I did so - don't remember 100% with certainty though). Yep, this is crucial since we need to know what exactly Windows is about to change.
3) Initialize the drive on Windows.
4) Just save it as a file, doesn't matter if its on another partition or not when its a file.
5) Compare changes between the two partitions/drives that were cloned to.
6) The very first backup, step 0, restore this back to the PS3 drive.
7) Once its restored, look at the file comparison (between the second and third backups) (not the 0), any changes should basically be in the first 1MB, only write the changes from the second backup into the 0 backup that was restored onto the drive.
And every should work.