I think I have a problem. Got this game for Christmas a few weeks ago and designed and printed most of this before I even tried playing the game. Card trays are pretty tall, but might make for room for add-ons (don't know what add-ons are out there, or if I'll ever get any).

Printed on my Prusa I3 mk2s fine. Only issue was the large card trays, they are exactly the full printable width of the bed (250mm), so I had to turn off any brim or skirts. Everything else worked fine with default Slic3r PE set to normal 0.2.

My initial design for the token tray had the cutouts a bit too small to easily get tokens out so I made them larger, I also made it a bit taller as I had miscalculated the amount of health tokens (they all fit but just barely). I'm not going to print again though just for those issues, if you print it and its still wonky let me know and I'll update.

I wanted to design it so you could use the trays in-game, and I think I did. I use the separators to keep track of discards and cards removed from game.

Print one of everything except the large card trays (x2) and separators (as desired)

Update: After a few playthroughs, I found it annoying to get the tickets, eldritch tokens and gates out. So I made some simple lifters, they should make it a bit easier.

I also made a basic lid to keep pieces from falling out if the box gets turned over.

Update 2: I really like designing for a quick setup wherever possible. Ideally you should be able to just lift out the trays and start playing. So I trimmed a few mm off the token/card tray , and added a lid frame. Print the lid and the frame, then, if you want to, glue the flat part of the lid to the flat part of the frame (you don't have to glue it, it fits fine, just makes for one less piece of clutter when playing. The frame allows for the character, elder one, reference and mystery cards. It works well for storage, but also does a nice job of keeping them neat during play. When fitted on top of the token tray, the total height of all storage components should be 54mm, which allows a good fit for the game board and manuals, and keeps all components in their spots.