It fits! Nearly...

After purchasing Vantage and he associated upgrades, I wanted to see if I could fit everything back into the box again. I found instructions on how to do this, but for the life of me couldn't find the post again, so here are my own photos.

The following results in a 5mm lid-lift, but includes:

All punched original components and tokens. (Story books, cards, dice etc.)
Upgraded wooden skill tokens.
Upgraded Metal coins.
x6 upgrade dual-layer player boards ('grids')

How to pack Vantage:

1. Base game tokens, money, and player tokens. By pushing the three stacks of large location cards to the left of their spaces, there is enough space to carefully insert the original component to the right of each large location card space (see coins, skills tokens, and player tokens below in their baggies.)

2. Upgraded tokens and coins, and dice. With the original tokens bagged and stored, put the upgraded skill tokens, metal coins, and dice into the green boxes. Put a small baggie on top of each box to keep things in place as you slide them into their spaces. When you get them out, place a couple of fingerson the plastic baggies to help keep things in place and avoid spilling everything as you withdraw the boxes.

Note the baggies on top of the green boxes.

Boxes safely inserted!

3. Boost tokens and character card place holders can sit flat on the top large card space, which has spare depth.

Silver 'boost' cubes in their bag (at top of image), lying flat, before the
secrets deck (in its pack) is laid on top of them.

4. Plastic card holders and secrets pack. The holders stack vertically in the storage space next to the card decks (shown at top left below.) The secrets deck (in it's plastic pack) can

5. Dual-layer player boards. All 6 player board 'grids' lie down flat in a stack to one side of the game card decks.

6. Book of Vantages and Book of Secrets. On top of the player boards, place down the 'Book of Vantages' with the spiral binding against the wall of the box. On top of that, add the book of secrets, but leaving a gap so it isn't on top of the spiral binding.

7. Rulebook. Add the rulebook on top of the book of secrets.

8. Game board. With step 5 ~ 7 done above, the main game board (really just a thin card) will lie flat on top of the card decks, book of vantages, and rules.

9. Storybooks. Insert the eight story books one at a time, putting the bound edge of the story book against the wall of the box. Do the same for each, but putting them down so there is just one against the box edge, then do the next one. This spiral of storybooks will slowly rise in height, but do this for all of them.