Just lost a detailed response $@#!, so short & sweet version - start by getting a Seachem Ammonia Alert - cost $10 or less. It monitors free ammonia (NH3). Uber important right now. Many test kits give false readings for NH3 when one is using Prime or Safe.
Keep the water clean, low nitrates, but don't over do it as I assume that your filter is far from being well established. That link I posted pretty much spells out what I know about HITH. The rest is still up to debate. The researchers still don't fully understand Spironucleus aka Hexamita, but when it becomes systemic and travels to organs etc, including the head region (as discussed in various papers) it can be deadly if not corrected. At the very least that fish is going to have some serious scar tissue down the road.
Those pits are being attacked by bacteria now, and you may have to consider a hospital tank, and some form of antibiotics. I would highly recommend watching the following two videos.
Sorry about all of your troubles over this past year!