The water separator I remember had a glass bowl on it and a round gasket above that sometime fell out. It would give some of the problems you are talking about.
Your fuel tank issues should have cleared up by now so I have to wonder where you are getting your fuel from. I've seen these problems many times with people filling 55 gallon drums at the station and hand pumping or pouring fuel into the tank.
Blowing the lines out with air pressure is usually what I do if I think there is something in the tank. Do you drain the junk off the bottom of the tank every once in a while. There is a valve for stripping settlement off the bottom of the tank.