Stinky Bun...

ok i love stewie to peices, i really do, but he is a stinky bun,his urine is back to smelling skunky,and even tho he only goes in his litterbox, it overpowers the house, i use vinegar and scrub vigorously with hot water and a scrub brush, and that helps for a while, he was eating russels rabbit food but i switched him to oxbow,wat else can i do?
a neighbor suggested peroxide and then a good scrub with hot water afterward,and then rinse, does anyone have any other tips?

Is he neutered? Have you checked to make sure his scent glands are clean?

he's intact as yet,i didn't even think his scent glands might need cleaned(he keeps himself pretty clean), i'll check today while i'm doing his nails.
thank you!