Scented stuff really makes a hamster mark their teritory more. I'm glad things are working out. I hope he is ok. You could use something that looks
like this for the bottom of the cage than put the regular substrate above. I'm sorry i'm giving you my country's product but i heard it is very effective for absorbing pee and smell. I'm sure you can find something similar. This product could be described as paper pellets (if that makes sense).
Also i clean the wheel every other day with water and i dry it with a cloth and that helps as my robo like pee showers every day.