I read somewhere that rodents either have very small or no bladders so they "leak" wherever they go. That is likely what you are smelling. Cleaning up the pellets are only half the battle. When my old TT got invaded, I steam cleaned the carpets and upholstery and wiped down every surface with disinfectant.
It is a dirty and relentless job as I had to remove the inspection panel under the shower, pull the furnace apart, remove all inspection panels, and pull all the drawers to clean behind and under them. They also got into the oven and shredded the insulation in places so I had to pull it and clean and re-wrap the insulation. I also removed the underbelly material and cleaned out the pellets under there.
Our TT was struck first when it was only 6 months old by rats at the storage facility despite the fact it was winterized and there was no food inside. That was a mess and my DW probably wouldn't ever set foot in it again if she had seen what I saw. The second time was at a different facility and the mice mess was significant but no where near as bad as the rat problem. That time the TT was also winterized with no food inside, We still store our new (to us) Class C there but have moved away from the edge of the lot where it abuts the woods and parked in the center of the lot. In 2 years we have had no rodent problems.
Also be sure to wear a mask during the clean-up. Hantavirus is not something you want to contract.
