Chronological Timeline

All of this should happen within a month, I think. There may be some flashbacks and backstory that will give the novel a basis in the history of this all, but, for the most part, it will be revealed as it is happening. We will need to know more about Phin’s previous life. We also need more about Gorse’s former life - how he became the man he is who rules The State with an iron fist. The antagonist backstory is as important as the protagonist backstory, so both will need to be revealed.
Phin will only be imprisoned for a few days the first time (they truly only let him out to follow him).
The second time, he may be imprisoned for a week, but he would be tortured, so he could not possibly take that for an extended period of time.
The most time that may pass - maybe this has to be longer than a month - will be the time that Phin is not with his family and is with The Alliance. At this time, he will be working on his weather controller.
Once the Alliance breaks him out the second time, things will have to move quickly. This portion of the story may only take two to three days. They will have to mobilize the entire Alliance quickly and strike before The State can be ready for an attack. The weather controller will be a major factor in this win. Not only will it debilitate The State forces, but it will also bring sunlight and weather variations back to Capercairn.

As with m first outline, this, of course, is subject to change. It will likely change a great deal by the end of November!