Last night I found a small sized plastic adjustable organizer used for screws, nails, ect. for $3.00 at Home Depot. It looks kind of like this:

I have sectioned the box to hold all of the following:
1 section for all character markers with stands.
1 section for Focus markers.
1 section for $1.
1 section for $5.
1 section for $10.
1 section for Stamina
1 Section for Sanity
1 Section for Clues
1 Section for Dice
1 Section for Activity Markers, Horror Track Marker, Explored Gate Markers.
1 Section for Doom Tokens.
1 Section for Closed markers.

I also ended up printing out "tuck boxes" from Boardgame Geek for all the cards, Monsters, and Gates. These work great. I discarded the plastic organizer that comes with AH because it takes up too much room. Now everything fits perfectly into the game box this includes the Home Depot organizer as well.