Yep. No clear idea how, or what I could have done more effectively.
I am/was on the last part of Chapter 2, went after a likely source of infection, went back home to deal with a sudden emergency [actually I didn't do that the first time, tried to do this sequence the other way around, and my kingdom was destroyed, but that actually made sense], then set out after the real source.
I even skipped resting, clearing fatigue with the lay-on-hands mercy.
Except... after numerous fights, I'm tapped, out of resources and half my party is quite poisoned (because wow, poison in this place, and some of these monsters are just ridiculous, even on normal's 'slightly weaker' aka actual pathfinder stats). But if I rest, my kingdom is destroyed because... reasons? I'm honestly not sure why, the game's lack of feedback and explanation is really very frustrating here.
The kicker is... I have to rest to progress. A thing needs to happen to put in another thing to get the poison to kill the threat. [Nothing actually explains that, by the by]. But that ends the game for me.
The kicker is, looking at my saves:
I've got one in my throne room, on the 8th of Pharast, 4711.
The next, is at the [redacted] fort, on the 9th of Pharast.
I don't have any saves for the second stage at home, but presumably that happened on the 9th/10th of Pharast. [And I tried not doing this bit, but that ended up in a fail state for reasons that seem more sensible. As in, my capital was depopulated/eaten in my absence]
I'm currently... in the final bit in the [], and it's the 11th of Pharast in my quicksaves.
Given the travel times involved... I honestly don't know how I could have done this without getting a fail state on the obligatory rest.
But apparently there is some sort of timer. And either I completely messed things up at the beginning of the chapter with the trolls (where I let quite a bit of time pass to get improvements done, the ones where you have to let your character AND an advisor spend two weeks spinning). Or just the final bit has a timer, but it's somewhere between 48-72 hours, and you've got three maps to clear plus some long travel times.
I'm not entirely convinced its doable, and a lot of these fights were just absurd and not particularly fun, especially in the final area. There are a lot of monsters, and the vast majority have poison, some with absurdly high DCs.
So... yeah. Have some griping. The biggest part is the lack of feedback and information. The game simply doesn't tell you things, particularly the kingdom parts. And while most of the timers haven't bothered me, an invisible one that can fail you on a rest you must take (for reasons that aren't clear, both why this part has a timer and why you must rest) is immensely frustrating.