One of the big problems is that my tap water measures 0.25 ppm of ammonia, so when I did water changes in the past, the ammonia readings would rise then fall the next day - which is what alerted me to this problem in the first place, when the readings did not fall. I have never had any readings of nitrate or nitrite on any of my tanks - ever.
Of course I use a water conditioner (Amquel+ and NovAqua+) but even my experiment of testing treated tap water (not added to the tank) there were still readings of ammonia, so I don't know how I can say what's been "converted to ammonium" and what is still poison "ammonia".
I still think there is something else going on with the tank, either bacterial or a parasite - I don't know if "skinny disease" is contageous since I'm sure that's what the clown loach died of and now the male molly is sick and thin this morning.
The fish aren't congregating up near the top either, which I thought was a sign that there was too much ammonia in the tank. they all prefer to hide on the bottom.
I don't know if not treating anything and just doing the daily water changes is going to be enough either, or if I should treat them, or even what to treat them with. I guess that I'm bad that way that when there are many options before me and I can't make a choice - I tend to chose to do nothing until a clear choice presents itself. Nothing seems clear right now.