I'm not sure how much I can help. You have a comparison with and without the save, so you know where the save is stored (looks to be location 0x2000).
I took a random save from our site, and the length is 0x8000
You could try to use Edit > Select Block (or Ctrl + E)
Start from location 0x2000, select length 0x8000, hit OK.
This will select all the data in that range, and you can copy it to a new file, and save that new file as a "test.sav", and see if PKHeX would open it.