Bob,
I agree that this could be disease related. However, I also think the environment is not ideal. I know some people have success with cannister filters, but I believe the filter media has to be changed or cleaned pretty often. As in, once a week or more. I personally do not have experience with using them so I can't offer much more.
What I'm thinking is that you have essentially two "waste traps" if you will. The first is your under-gravel filter. You are pulling waste from your water column into your substrate for it to be trapped. I know you are vacuuming the substrate, but I'm assuming this is when you were doing water changes every 3-4 weeks.
The second "waste trap" would be the cannister filter. Again, depending on how often the filter media is cleaned and/or changed, you may just be running water through this decaying waste that isn't actually leaving your system.
I would start by reversing the flow of your under-gravel filter. You don't want too fast of flow though, somewhere around 150gph or a little below through each filter plate. I would also, remove the cannister filter and replace it with a protein skimmer. I'd save the cannister filter though and use it when you vacuum the substrate if you can get it to work for that.
Your tank water will probably look stagnant after this, so I'd throw in a cheap powerhead or two from
amazon to keep the water moving. This will also help with waste and detritus from settling on the substrate.
You can use biospira, microbacter 7,
fritz, or Dr Tims for some bacterial filtration. Or some of each. There are plenty of other options though so that list is not exhaustive.
I'm still skeptical of your well water too. If you can, look at adding a RO/DI unit just for your fish tank water. RO Buddy on
amazon has some more affordable options that work well.
With the new rock, you're going to have a lot of cyano blooms down the road, so be prepared for that. You might want to try the other steps before you take out all of your old rock to replace it.