Sounds to me like you're doing a great job. But honestly I would not use Permethrin as a preventative on baby chicks, for something that might not be happening. A dust bath is always the way to go to help them rid themselves of bugs unless you truly have an infestation to deal with. It doesn't...
Do you SEE mites or lice? Chicks itch/preen alot as feathers come in and fluff comes off. You could provide them with first dust bath. Also, pasty butt is not normal.....