Anyone who has the game knows that organizing the expansions and all of the content is no easy task with the stock insert. I built this a while back but just recently took pictures. I used the plans someone made here https://boardgamegeek.com/filepage/129695/box-insert-plan-store-paper-assets-core-game-and-e as a place to start. I modified them slightly though, but they're a good place to start. I used foamcore from a local craft store (about $10) and an hour or two with a glue gun.
When you take off the lid, this is what my game looks like. I liberated some ribbon from my wife's wrapping paper pile to make handles (sadly there was no black ribbon).
For tokens, I adjusted the insert so that I could fit them in while encased in coin collector cases (from amazon). Beneath the tokens, terrain tiles, dice and books, the board sits. A simple ribbon is placed under that for ease of removal.
The bottom layer has all of the game cards. The middle portion was where I'd originally stored all of the gear, but in this photo about half of the gear cards are taken out and put in a binder (waiting on the rest until I get (long shot) my Mage sleeves pledge from kickstarter. This is all of the current cards, sleeved in FFG green sleeves. The old gear spot will be repurposed for more expansion cards in the future for wave 4 and any overflow will end up in the 1.5 upgrade box I kept. I'm debating turning the 1.5 box into the 'game box' where I'd move all of the current cards for whatever campaign I'm doing and use the larger box for storage.
This little box contains all of the game components needed during showdowns; terrain, vermin, strange resources, disorders and fighting arts and was made to be removed and placed beside the board for ease of access. The rest of the cards stay in the large box and I can just reach for the deck needed for each encounter.