So what this problem basically boils down to is physical damage to the eInk display driver chip on the board, and potentially the flash chip on the display itself as well. In your case, Zirowe, it's probably just the chip on the mainboard, as you've replaced the screen.
It's not recoverable through any software means. And depending on where the damage has taken place, it would be no small task to try to fix the physical issue.
FWIW, I tried using the unbricking method to revert to v3.0 of the software and make sure that I wasn't dealing with a software corruption... no dice.
I have no idea if this approach is even reasonable, but I even tried running my heat gun over the mainboard (separated from the rest of the kindle) to see if maybe I could reflow the solder and repair any cracked connections. It didn't make any difference, but I'm not even sure I had a successful reflow.
It would be awesome if any professional EE types wanted a fun project to see whether a physical fix is possible, but the payoff is most likely far below the effort required to sort out a solution.
I'm ebaying for a new kindle