I would try increasing your nutrient strength by 10% every few days until the problem is fixed. I would suggest watering for 15 minutes 4X per day if the girls have good roots. If rot is a concern, I'd throw 2ml per gallon of 35% peroxide in the soup. For fungus gnats, I've added a 1/2 inch layer of washed sand as a cap on top of the pots, the gnats can't get through it and the larvae die.
Hope that helps!
Hope that helps!