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You could potentially give a siege ability modifier which allows GB or whomever you are declaring independence against to have an easier time occupying the territory.
If you are going solo in the independence war, you should perhaps include a morale of armies of merely just a +5% in the America Alone modifier. Make it fairer for the player
This post isn't merely just to complain though, it's clear you put thought and hard work into the mod, with all the flavour events and possibly even after the independence war even though I hadn't gone that far yet. Even if it is a little pet project, I just want a more enjoyable experience and some little tweaks like these would go a long way.
I guess I'll also mention I structured the events and such so that you don't neccesarily have to start as England, but anyone who makes a colony in East America. Although doing it as England would get you the best experience.
The event chain will begin once you reach 50% liberty desire, where after you have to keep increasing it until you reach 90% where the war will begin.
As for the gaining churches thing, that is just a colonial nation thing it's always like that because the meantime is based on province not tag, so its far more likely to happen with more provinces owned.