Thanks everyone!

Sounds like I'm doing the right thing - more or less. So I guess I'll keep doing that for now. RE copper heating elements in the water heater: yes, that's what I remember hearing might be affected by the chlorine. I think I won't worry about it too much though - even if chlorine in a spa could eat through copper after a while and even if my concentration during the shock is higher, it's only for a short period of time (a day or two) and after that the water is clear again.

As for preventing the problem from recurring... I get the impression that the bacteria get up to a noticeable concentration in two ways. 1) They get in through the groundwater - nothing you can do about that - though perhaps one could filter or treat the water between the well and the plumbing system 2) shocking the well gets rid of most of them living in the system, but the few that remain start reproducing and spreading after that. I don't know which avenue is the primary one via which the concentration of bacteria gets up to a noticeable level.

The good news is that this kind of bacteria, while annoying, produces no known deleterious health affects (that I've ever heard of). Its just a nuisance.