I think you're over thinking it, but it's been a while since I've had my set-up. I'm sure some of the fish tank guys will come in with some insight on tank starter products you can get at the local fish store (probably not so local for you, heh). I'd think that well water would be better than city tap water, but I might be concerned with the amount of minerals for where you live. I think when I set-up my fish tank, I just poured a few ounces of whatever tank starter into the tank so I could use tap water. Years later when I added the aquaponic set-up, I didn't do anything at all. The fish waste is already in a state that the plants can use, which is the whole idea of the system. I'm interested in seeing how you address your system as far as using a bell siphon or timed system or whatever, so I'll be checking in to see what you come up with.