If something's clean as a whistle, that doesn't mean it's shiny and spotless like a silver whistle in a referee's mouth. The idiom refers to a whistling sound: That piercing noise is super-bright and finely edged on the ear. This is part of a complete episode.
"As dirty as a toy store whistle." I had to laugh with you about being just the right height. When my son was about 4, we walked into a men's room at a restaurant. The restroom was narrow and as we walked, single file, past the urinal, he spotted the pink deoderant "puck" and snatched it out, asking, "What's this, Daddy?"
With a couple in the low-water bridge below my dad's house, this summer's deluges has a whole different connotation on the concept of a clean whistle. I have had to clean their openings several times to aid the water flowing under the road rather than over the low-water bridge. Several times it was unsafe to cross and one should "Turn around; Don't drown."
So, "clean as a whistle" means something entirely different in this context.