Hi J.! We went through this with my three year-old, and I am so sorry! I know how upsetting and scary it is. I blamed my self (I'm not the world's neatest housekeeper - who is with kids?) but my house is a clean safe place. Suddenly it felt like every corner was harboring some creepy disease. All of the suggestions you received were good ones, but I'd like to add a couple of things just for you to think about.
My daughter ended up seeing an infectious diseases specialist at Birmingham Children's Hospital (wonderful!) and one of the things he said that was a contradiction to what we'd already been told was NOT to treat skin infections with internal antibiotics unless they become extremely deep and serious. He said the antibiotics should be reserved for deep infections and internal spread of the infections, as the skin lesions usually resolve on their own with the right care.
I know! Sounds crazy, but he told us to do everything you are doing and to treat the spots with an antibiotic ointment (Bactroban is preferred) and cover them only if they are weeping (to stop the spread). He said not to keep her out of school and put long pants on her only if we felt we needed to keep the spots clean (or if she messed with the spots or felt self-conscious).
Not using the internal antibiotics for the infections prevents overuse, so that when your child really needs it, the antibiotics still work for her. He also said newer studies have shown that the nose ointment is not very effective, so if your daughter fights that part, I would consider talking to your DR about that. He gave us lots of info (he knew the newest information on treating it) and really set my mind at ease. He also advised that we keep my daughter's eczema in check as much as possible, b/c eczema kids appear to be more prone to the infection. Lots of moisture, cooler baths, all the things you use to help the skin stay moist and healthy.
I'm sure you've gotten great advice, but the #1 thing I'd advise is to try and see a pediatric specialist in infectious disease. It was well worth the time and money (an overnight trip for us) to talk to someone who specializes in the problem and was wonderful with my child!
Good luck and hang in there!