I have some experience in home aquariums, but my largest tank is only a 125 gallon. Nothing to match your 4000 gallons. However, I do have some input to your problems.
The first thing I noticed when reading your post was your ammonia and nitrite tests. 0 ppm ammonia is good, but in a stable tank, NITRITES should be at 0, and NITRATES are the only thing that should be in your water. Nitrates themselves in low numbers are good because they cut down your fish waste, and mean that your tank has fully cycled. However, if your water is not changed enough, and fish waste is just left to sit, they can accumulate over enough time and high numbers of NITRATES can easily kill your fish. Anything smaller than a decent sized pond is not self-sustaining and does need to be taken care of.
Please do a test on NITRATES and post your findings here. Your tank may not be fully cycled, or is and the water isnt be changed enough.
The second thing I noticed was that you didnt mention if you had conditioned the water to get rid of the chloramine and chlorine if you used tap water prior to introducing the fish. Both can kill your fish as the chemicals eat away at the gills.
Bruce is right on about the oxygen. With that high of a fish load, oxygen is a worry.
"New Tank Syndrome" is the common term that aquarists use for situations similar to this. Maybe I can find some links that explain cycling, and ammonia, nitrites, and nitrates better than I can.
- Jighead
