Totally new to this, but built same E/F system with some slight changes in looks. You should have no water remaining in the system after the pump stops and starts to back flow. It should drain entirely. Really curious how any water can remain in there.

I'm putting together what I think is a dank grow room right now... looking forward to my tomato seeds getting here in about a week to start off.

Fix your E/F system so no water remains or you will have issues with either root rot, or something growing in there you don't want.