Yvonne
What are you doing with the poop when you find it?
Hopefully you are putting it in the litter tray and then gently placing Homer in the tray, I also take hold of a paw and get then to try to cover it.
Having recently been through hell with the phantom piddle and poopers I empathise;one thing that helped also was changing to a soft paper litter.The two kittens who were still dirty were put in a pen full of litter trays which were gradually reduced. All now clean but its a gradual process of reverting back to the wood based litter I normally use.
Also much as I felt like crying I smiled about it and wrote it all on a thread,it really got me through.
Vet check is advisable,its just possible he associates his tray with pain.
Good Luck,you`ll get there in time