I finally solved the issue of storing Cosmic Encounter components. I love the game, but the box doesn't hold the components well, and I forged forward trying to resolve that. I think I succeeded.

All of the containers in this thing were generated by the scad files from other projects, and you'll also need to download the ship stacker separately. The components you'll need to print are:

Cosmic Encounter.stl: This holds the cards. This container has three compartments, to hold each of the three decks. This was generated by lufton's Customizable Card box, https://www.thingiverse.com/thing:2404395

Cosmic.stl: This holds the Cosmic Tokens. It was generated by michalhoudek's Box With Cover and Division, https://www.thingiverse.com/thing:2807163

Planet.stl: This holds the planets and colony marker for a single player. You'll need five of these. This was also generated by michalhoudek's box maker.

gubbins.stl: This holds the rest of the chits and such. This was also generated by michalhoudek's box maker.

In addition, you'll need to print five of zcontest's Cosmic Encounter Ship Stacker / Storage, https://www.thingiverse.com/thing:2088019

To fit everything in the game box, you'll need to fold the left side (opposite the deck holder) of the cardboard insert under, to remove the spacer on that side. I included a picture of the insert to make this more clear (I hope!). Once done, everything fits very well and snugly!