Do you have pictures of the white patches? Before looking at the water I would want to rule out the possibility these are secondary infections from an external protozoan parasite. Has this problem coincided with additions of new fish. Snails?
I've got well water and since there is never any chlorine in the ageing barrels, I have learned to be careful not to introduce any 'live' water from the tanks on equipment, or my hands, that might contain bacteria or protozoa. The barrels seem to need less frequent cleaning now, about every 6 months. That's one thing you can do although it might not solve the problem as it could be from the well itself, or the pipes. Older wells aren't lined or capped very well.
In my water barrels that jelly-like slime only collects on some types of plastic, the heater cords and air lines. When I look at it in the microscope I don't see anything that looks like bacteria. I think some harmless substance is collecting there, probably from static charge, although it does eventually become a substrate for microbes.
Usually the bacterial tests for well water are only testing for coliform bacteria, which can be harmful to people but not something to worry too much about with fish.
You might also consider shocking the well with bleach, as described here:
http://aces.nmsu.edu/pubs/_m/M115/welcome.html
What I would do if this problem persists (and its not from a parasite) is set up a strong UV sterilizer on the incoming water line at the ageing barrel, with a 1/4 line and a throttling valve so that the rate of flow through the UV can be kept very slow. The flow would take maybe three hours to fill a 50-gallon barrel, with a float valve. This way all the water going in would be sterile, or as sterile as the UV can make it. I thought about doing this but there is so much nitrate I just switched to ro instead.