over cleaning the cage might precisely be the reason why it smells so much. If they don't find their odor on their territory, they will mark even more agressively, hence making the smell stronger.
I just wipe the bars and ground everyday, but I only clean once a week (and I do it only one side at a time, not whole at once), and I don't have smell issues (and all my males are intact. Yes, they do have a smell, like all animals including humans, but not worse than a dog)