Well one clown has died.
The nitrite level was likely too high. I did another partial water change just now and will test again once the waters have mixed a bit more. I am a bit disappointed but not discouraged. I am just going to learn from this mistake. I hope the other clown makes it. If not, I will wait to see the nitrite level stay zero for several days before adding another fish.
BTW I have set up a Berlin system with a plenum and a deep sand bed. I am using live sand, base rock and a bit of live rock.
Also, I solved my problems with the Berlin skimmer - turns out I hooked it up wrong!