Killa, the way you describe is the way most mouse breeding is done.
Other than cleaning, Its a low maintenance dream... I don't really understand all this messing with seeds and stuff that can't be hopper fed.I guess that's Ok if the mice are also pets but it sounds like a lot of work, and you're quite right, they wont eat soiled food.
I fill my Lab chow hoppers about once a month, and that is it for feeding.
For weanling holding bins I use big Rubbermaids, and I make screen baskets for the chow and that keeps it out of the substrate