Minor Update:
No deaths since the last water change after the black neon tetra died (about 10 hours). Everybody looks happy right now, although they are sleeping for the most part (1am here).
I also changed out the filter medium in the magnum 350 that I use for mechanical filtration and put in 16 oz of activated charcoal (usually it's just filled with floss). I also run a fluval XP3 as a biological filter. I don't know if the charcoal is helping or even will help, but I figured it couldn't hurt of there was some kind of a chemical or other toxin that the tests werent detecting.
I also removed all of the large pieces of lava rock that I had in the tank as decoration. I'm going to boil it tomorrow on the off chance something evil is lurking within it. The pieces are about 12" in diameter so there are lots of pores for things to dwell in I guess.
Finally, I raised the tank temp to 82 from its normal 74 hoping to boil of any pathogens that might be lurking. I'll lower it back down in a day or three.
---
Currently, this tank is unplanted. Getting plants in this town is very difficult because all of the fish stores have absolutely DREADFUL plant stock that is also very expensive. It's usually so full of snails and black algae infestations that your tank ends up looking awful.
That said, as soon as I can get some more-pristine stock (and stabilize this die-off of course), I am planning to plant the tank.
On the topic of substrates, I've found sand, while it looks REALLY nice, to just be too much of a hassle to keep cleaned. I've found that with gravel, whether large or small grained, it is much easier to work with (doesn't get sucked into the gravel vac). Of course, that really only applies to freshwater tanks. I have a 120G reef tank at the office that has a very nice deep sand bed both in the tank and in the 40G breeder it uses for a sump. The clean-up critters there serve to keep it looking good.
I've never heard of any issues that magicly crop up with large-grain gravel beds over small. I have heard that a freshwater tank that has sand that is too deep (over 3 inches or so) can lead to problems with toxins building up in certain areas (whereas in a marine tank, the various critters serve to stir it up so you go 5" or so for a DSB). I have no real evidence of this, just ghost stories told late at night around the fishtank.
If there are any more thoughts or ideas, I'd love to hear them. I plan to do another 25% water change out tomorrow (I've always used slightly salted water, about 1tbs/10g), but I'm trying to avoid dosing the tank with any chemicals/