Your aquaponic made me think of how to do it in a bigger scale. So that means no shelf and having 2 pumps pumping back and forth. I wonder if it can be done with one pump.
I have a feeling you'll need to add extra ferts or feed more to the fish. Have you checked no3 , po4?
Some people dose extra Iron, epsom salt and seaweed extract.
Bigger scale: I have 2 IBC totes with the top cut off 200 gal tank for fish tank and top part as bedding. Works perfect, but I need more beds for the amount of water.