I don't think there's any reason for concern. This is just what MTS do. They
are nocturnal. As soon as you turn off the lights, they emerge from the gravel
and go in search of algae to munch. Mine do this every night. (If you turn
the lights on again, they will fall back to the gravel in a panic.)

I'm concerned that since I started a Hagen CO2 system today that the water
parameters have changed too drastically. My Ph went from 7.6 to 6.4.

That's too much CO2. You should increase aeration in the tank. Aim for a pH
of around 6.8.

When I woke up
yesterday, my clown loaches were poking out the top of the water (apparently
for air).

More aeration will help with this problem.

My loaches used to come out all the time when I had
a cheapo 15W fluorescent. Now, they hide all day with the 55W PC I have
running.

Loaches prefer dim lighting. However, they'll adjust, especially if there are
plenty of plants to hide among.

It seems that most people advised not to try to stop the CO2 at night. With
a yeast system, this seems impossible anyways. I was wondering if it would
be beneficial to turn on an air stone from a pump though. That might help.
I definitely didn't enjoy the sight of my clowns bobbing for air come
morning.

Increase your aeration/surface turbulence. A powerhead would be better than an
airstone. You can control how much CO2 stays in the water very precisely with
a powerhead, just by aiming it for more or less surface agitation.

Some people put the powerhead on a timer to go on when the lights go off, but I
think you'd be better off leaving it on all the time. You have too much CO2.

Eventually, when the plants are growing better, you may not need the powerhead
any more. But if you just planted the tank two days ago, you can't expect the
plants to provide enough oxygen to last the whole night. They are in shock at
being transplanted, and will need a few days or weeks to get established and
start growing well.

Leigh

http://www.fortunecity.com/lavender/halloween/881/