Hey guys! Thanks for all the suggestions. Here are some of my answers:
The tank is pretty mature. It was first filled in March of 2011 and is well past the diatom stage and pretty mature at this point.
The otos have been in the tank for almost a year, I think, so it is definitely NOT the acclimation period or the caught otos being treated with anything. These guys have been in there for quite some time and 2 deaths in a week is scaring me.
As for how many there are, there are 2 remaining now after the 2 deaths, and there were 6 initially. I think one died during acclimation, but I can't account for the other one.
I don't believe I'm overfeeding the fish. I feed once a day, and all the food is gone within a minute or so. Anything that falls to the bottom is for the 5 corys in there and 5 Amanos to clean up. There's also tons of MTS on the bottom. I realize that since I have so many plants that the nitrates should be low, especially since 1/3 of my surface is covered with mini water lettuce, which should be a nitrate sink. I'm not sure why it's so high all the time, but I do run low light, so the consumption is not as fast as with higher lighting. A lot of the plants are also slow growing (~15 crypts, an anubias with like 30 leaves, java fern, tiger lotus, all slow growing), but there are also some relatively quick growing plants in there too, including a bunch of jungle vals, blyxa, Ludwigia, Hygrophila, and HM).
edit: Oh also, I had been feeding Repashy soilent green before, and I stopped for many months when I last ran out. The otos (and the Bolivian, corys, and cardinals) really love it, so I have resumed feeding it. Maybe they didn't take to the Ken's veggie sticks as well, and they were starving out? Otherwise, I'm out of ideas if it isn't the nitrates... All the other fish are fine, including the shrimp too.