I have just the base game of Mansions of Madness 2nd Edition (with no intention of getting any expansions so far) and couldn't find any one insert that quite did what I wanted, so I compiled bits from lots of other brilliant inserts and added a few pieces to make one complete set including a dice tower for added fun. This requires all monsters to be based, mine are on clear acrylic, but it allows space to hold the old bases and info tokens for the monsters separately as well. It also supports vertical storage. I kept the cardboard insert as a base for the art on the bottom, then all manuals etc sit on the top after all the trays. See the layout thumbnail for how everything fits together in the box (yellow items are ones I created/remixed, other two colours are exactly as I got them from err404 and manuelf).

You need to print one each of:

• Card Tray and Cover (from err404 https://www.thingiverse.com/thing:1920453)
  Holds all cards in sections, plus clue tokens. I believe supports sleeved cards, but see original design for details. Sits on top of the room tiles holder in a corner

• Tile Features Tray and Cover (from err404 https://www.thingiverse.com/thing:1920445)
  Holds all doors/barricades/paintings etc. You do need the lid as the spacer I created is only sized to hold the lid on in the gap it sits. Sits on the bottom of the box in the space not taken up by the room tile holders.

• NPC Tray and Cover (from err404 https://www.thingiverse.com/thing:2170822)
  Holds all people tokens. It's larger than it needs to be for the base game, but the extra space isn't an issue. This sits on its side between Old Tile Holder and Medium Monsters, so you do need the lid.

• Dice Tower and Tray (remixed from zepmaster https://www.thingiverse.com/thing:2784780)
  My remix is just to scale down the size slightly to fit into the section of the box needed. Still fits all dice through it very nicely. The tower lays down on top of the card holder and the tray goes on top of the small monsters.

• Tile Holders A, B, and C (from manuelf https://www.printables.com/model/155571-mighty-mansions-of-madness-organizer-trays)
  These jigsaw together at the bottom of the box to hold all room tiles. There are additional tabs/grooves in it as the original design had multiple of these layers for expansions but they don't have an impact.

• Star Spawn (from manuelf https://www.printables.com/model/155571-mighty-mansions-of-madness-organizer-trays)
  The side of this with only 2 spaces holds the Star Spawns, facing next to the card tray. The other half is used to hold the Old Tile Holder. Goes in the bottom corner on top of the room tiles.

• Medium Monsters (from manuelf https://www.printables.com/model/155571-mighty-mansions-of-madness-organizer-trays)
  Covers all the medium monsters like Riot etc apart from the Hunting Horrors that have their own section. Sits on top of the token holder.

• Small Monsters (from manuelf https://www.printables.com/model/155571-mighty-mansions-of-madness-organizer-trays)
  Holds all the people minis like Cultists etc. Goes on top of the small box spacer and tile features tray.

• Investigators (from manuelf https://www.printables.com/model/155571-mighty-mansions-of-madness-organizer-trays)
  Holds all of the player character minis with loads of space. Lays on the top of the box above the Star Spawns.

• Hunting Horror Holder
  Mini holder just for those two Hunting Horror so their wings don't clash with anything else. Sits on top of the dice tower tray.

• Old Tile Holder
  Completely optional and can be ignored if you threw away the original black bases or monster info squares, but it fits in the other half of the Star Spawn holder.

• Small Bottom Spacer
  Ensures the lid of the Tile Features tray stays on while stored vertically.

• Token Holder
  Holds all search/explore/fire tokens and uses the investigator cards as a lid that is held in place by the medium monsters sat on top of it.

• Top Box Spacer
  Goes next to the Investigators to keep everything from shifting around when stored vertically.

Photos of how everything sits in the box now uploaded (though I still haven’t got round to attaching my bases so minis still bagged). My print is hashed as I use no walls/top/bottom to save on filament, though on reflection I wouldn’t do this for the Star Spawn one for stability and I had to do the people tokens box solid as well (plus obviously the dice tower and base).