How do you control the water level in each section?
I used these 3" rubber pvc endcaps cut in half so you can take them out as needed. You gotta play with them to find the level that suits your needs. But the good thing is, once the roots have developed, there's almost no need for them except for in the event of a power outage. But for that I bought a surge protector with a battery that will last a few hours running the pump. The roots themselves will also cause a little damming of the water as well, so it works out well where you can kinda just run the pump. With the battery pack, the only thing you have to watch for is pump failure.
Shouldn't you have drilled the holes for the pots on an angle so the plants don't grow straight up?