The zoning aspect is interesting. Out of city limits (at least where I live) generally you don't have zoning.
For example, I'm in city limits. I would be zoned as R1, except I'm in a PUD (Planned Urban Development if I remember correctly) and those are basically communities with their own guidelines (mine is set by our HOA, which sucks). However, my parents aren't zoned anything because they are out of city limits. They live on acreage, but even if they didn't it wouldn't matter. They can have chickens, horses, cattle, dogs (loud dogs), etc.
Agricultural zoning is two fold, it protects some land from non agricultural uses (so that a city/town has some later and doesn't lose it all) AND it moves ag related stuff away from people that it would annoy - spreading manure, noise complaints, general nuisance suits.
(I tried to copy and paste the thing I'm reading on ag zones that some guy wrote from Penn State, but I can't so here's the
link )
Your city has failed miserably at this, obviously.
I can't remember if Spock and the chickens are on the ag zoned area, but I would put them there (even if it's just toeing the line) because at that point it really is the city's fault. I'd try forcing them to either stand by their zoning, or force them to change it (which, yeah, isn't the outcome you want, but I think you'd still have legal recourse after that because you bought that acreage
because of its zoning)
I may have the facts wrong though, I get confused with so many people posting. I know you've said different things as you've learned more about the zoning etc.