5 1/2 hours might be to long of a time. One of the reasons why plants grow faster in hydroponics is that you are force feeding them every hour or so with
nutrients and with dirt the roots have to go looking for nutrients in the dirt. The plants will only use as much nutrients as they can absorb so you have to make sure you give them plenty.
The air stone goes in the tank and only needs to come on when the
pump does.
Ron