Hi R.! I totally understand the "is it a virus?/is it an allergy?/is it a secondary infection?" dilemma. My oldest daughter went through a period where we dealt with the same thing. Here's what we did:
1) Do NOT spray Lysol around the house, thinking that you're getting rid of "sick germs." I say this from experience because I used to use Lysol. Lysol is an extreme lung irritant and only makes the problem worse.
2) We did have our daughter tested for allergies. She was 4 at the time, and all the tests came back negative. Our allergist told us that at a young age, the tests sometimes are not accurate and that we might have her tested again at an older age. I'm not sure if this is the case for food allergies, however. You might ask your pediatrician if decreasing her milk intake would be advisable for a while. Milk has a thickening effect on mucus in the body.
3) Expectorants were always helpful during these episodes. They actually thin the mucus and help rid the body of that yucky stuff that's hanging around. Also, we only gave a suppressant at night and only then if the cough kept her awake.
4) We got rid of all harsh chemicals in our home. Bleach, ammonia, and other cleaners/detergents are so bad for our bodies and immune systems.
5) Daily mulitvitamin, vitamin C (our bodies can handle more than the RDA), and LOTS of water.
Since your daughter is/was running a fever, she should finish her antibiotics since there may be a secondary infection. I've heard that walking pneumonia/bronchitis is going around, and that should be knocked out (as much as I try to stay clear of antibiotics if we can help it!). Hope this helps! Blessings to you.