wvmarle:
For a project like this it probably makes sense to break it down into several sub-projects, each with their own controller.Like one that takes care of the chickens (food, door, lights).
One that takes care of your aquaponics (reading the many sensors, dispensing fish food, dispensing the needed extra nutrients and other additives).
This way you will make maintenance easier, and probably make the programming easier as well.
I think this might be the ticket. Going with multiple controllers. The only thing that I didnt want to have to do is get two controllers, and 2 RTC's. But I am thinking that if I rethink my hardware deployment I can bifurcate the SCA and SCL signals to multiple controllers or use one as like a "stratum 1" and have the other controllers sync time to it.