sounds like urine has soaked into the wood. if thats the case theres not much you can do. you can mask the odor but youll never be able to fully clean and disinfect the wood. if i were you id get a pvc or plastic set up or a tub or even an aquarium.

simply vacuuming the visible poo isnt going to get the urine out of the carpet. if you like the carpet id get at least another one or even a couple more so when you are cleaning your tank youll have a fresh carpet ready to go while the soiled carpet is being cleaned.

good luck