Each Faction box model comes with a lid. The Tokens box has a separate lid file (due to size constrains on my Thing-O-Matic). Print everything at 100% solid infill. Sand the lip of each deckbox down so the lids fit (not too much, they'll come off too easily). Fill with cards. Each faction box holds 50+ sleeved cards. Should be plenty of room.

You can print in any color you want, I chose purple and green because I like the color scheme of the original Netrunner CCG. Blue and Red would probably be more appropriate for this new version.