I've designed a couple token organizers to fit in the space left by the punchboards and I've decided to share them here (Upload pending approval).

There are 3 trays in total: two that go on top of the transparent lid and are kept in place by the foam (board and manuals go on top) and a third small one that goes alongside the miniatures tray.

Photos here: https://boardgamegeek.com/thread/2541024/3d-printed-token-organizers

UPDATE: Added 5th character tray.