Here are a few I've thought up (although I don't use them yet). I just posted this in another thread, but then I thought, this might make a fun topic if other people contributed their ideas too:
For the Dunwich Horror, there are two really easy ways to add to the threat. Have monsters spawn double on gates outside of the main town of Arkham (even if you're playing a team of under five), and the second one is have monsters that go into the Innsmouth vortices also add to the Dunwich track. You could do vice versa as well, but I'd imagine you don't want to make the Innsmouth track even *more* annoying ;') (And of course, you could also add the Dunwich Horror herald to make it even more challenging).
As for fixing the act deck, there's a very easy way. Whenever you draw an act card and do not return it, roll a die. On a 1, or a 1-2, or a 1-3 (depending on how risky you'd like your games to be), draw another one. Personally, I'd make it a 1. I wouldn't want *too* many games to be shattered because of drawing it.
Unfortunately, I can't think of an easy way to allow exhibit items back in the game (perhaps you could allow investigators to draw one for the price of five dollars at the magic shop, but only if the terror level is at five or higher— that way it can't be harvested for the Elder Scrolls easily, and it won't see play *too* often, but it won't be almost completely out of the game as it is now).
As for cult encounters, you could make a house rule so that investigators could trade five (or ten) toughness worth of trophies at the Woods, Black Cave, or Unvisited island and join the cult instead of having an encounter.