The Arkham Horror toolkit is a pretty good app. Maybe a bit pricey for buying all the expansion content, but thats fine.
I know that the setup and rules can be varied based on the number of players in the game, and which expansions are in use. The cards included in the Miskatonic Horror expansion that display the gate limit, outskirts limit, and monster limit help.
Why is that information not within the toolkit?
I propose that the next time the toolkit is updated, you include a flexible copy of the rules and setup steps. Maybe go as far as adding notes on how the various heralds modify the game. Give a step by step FAQ for how to run each phase. (ie, if Kingsport is in play, make sure a reminder for moving the rifts is in the list of to-do steps). If the Curse of the Dark Pharoah is in play, then put a step about managing the Ancient Whispers encounters. (No idea how that works since I do not have revised version of Dark Pharoah).
When playing Arkham Horror, there are many things that are easy to forget. Some easy to reference checklists would help. Putting them in the app keeps the list small and minimizes the wall of "If X expansion is in play, also do Y" things.