I know this is an old thread, but as a licensed welldriller/pump installer, I wanted to add one easy thing to watch for - old or broken well caps. New style caps are tight fitting and gasketed (aka vermin-proof). Older style caps have enough of a gap to let small critters like worms, caterpillars, etc into your well. They fall down into the well and rot. There is your ammonia. Chlorinating won't help either. As the animal continues to rot, the ammonia will just come back. I've seen wells full of acorns from squirrels, and have pulled out many mice and even a dead bird once(of course that well was a friend's and the bird came out with his wife and kid watching?

). Well height above grade is a big factor as well. Here in WI code requires 12". With an old style cap, it is even common for grass clippings to get in the well, which again can rot and cause issues. I actually prefer to leave the well height more around 16" if practical/ possible. Not saying this was the OPs issue, but it's possible, and any easy thing to keep an eye on. Chris