Wow well done you for getting him through all that. What sick ****** would beat a 2 week old kitten
I hope you do find a solution to his problems, after all you have been through together it would be awful to have to give him up.
Even if the tray over his favourite pee spot is in the way, it might be worth trying for a bit, just to see if you can break the habit, it doesn't have to be long term.