Well adding a new batch of CO2 and stopping the surface adgatation at
the same time caused a CO2 spike. The spike happened at the same time
the lights went out so the plants were no longer using CO2 and no
longer producing oxygen. So basically there were two problems.

One is that the increased CO2 in my soft water (4 dKH) caused an
immediate pH drop.

The second is that no surface adgatation + no plants producing oxygen =
no oxygen.

So basically none of the fish could breathe and the pH has crashed. The
worms all came up to try to get more oxygen and I would guess that it
was the pH that killed the shrimp. The reason only two of my fish were
showing signs is that they are the two that sit still on the bottom of
the tank most of the time so they have the least water flow over their
gills. The other fish still had enough air to breathe - they were far
less active than normal but they weren't dying. The flounder and goby
were having some serious trouble breathing.

To correct the problem I immediately started up the filter again to
stir up the surface and I added an air line to increase the oxygen
content. Within an hour everyone was breathing normal again.

The pH took a little longer to correct - I mixed sodium bicarbinate in
very slowly raising the pH by about 0.2 per hour. But the pH wasn't
really killing anybody - it was just the sudden drop that hurt them.
Keeping the fish at a pH that low would definately stress them but I
wasn't worried about it immediately killing them. Mostly the lack of
oxygen was the dangerous problem.

Everyone is healthy now though.

-Daniel