Since you suspect the water quality or contamination of the well, have you had a water sample tested?
It is not our house or well, so we haven't tested it. Our friends who own the place seem to think it is sporadic contamination, depending on rainfall, the local deer habits, etc. We just use the house for a week or so at a time and don't mind filtering. Before that we were shlepping all our drinking water in.
My only issue with the system, is you need to pickup the upper section to see how much room is available in the lower/filtered section. I think the Berkey system is no different.
I agree that is a bit of a pain. I am too lazy to look it up right now, but I seem to remember Berkey has an optional sight glass spigot that showed the water level, and would solve that issue. I also think it may be interchangeable with Aquarain.
David