I did a little DIY project I thought I might share in case anyone else was interested. I have been working on a print-fold-cut insert for the core game box and the expansion boxes that is designed to hold all the tokens from the game as well as the oversized cards for storage.
I can never seem to get a graphic to add to these forum posts so here is a link to what the basic top view looks like.
http://www.boardgamegeek.com/image/1489197/logan_mann
It is not printed with the sections colored...they are colored on this graphic to show the separate pieces that are folded and assembled. It does print with the graphics for which tokens go where on the sides of their respective compartments though for easy identification. When put in the box they hold each other snuggly so there is no required need to tape or glue (though you'd have to if you want to pull them out for use separately). The modifer token sections are 1 in deep leaving space to hold the oversized cards. The rest of the compartments are 1.5 in deep so they are snug with the lid closed. The large green section shown at the top of the graphic is used when fitting any expansion box...the rest without that fits the original core game. Should Vengeance have additional materials that are not just more of the tokens shown I'll hopefully be able to make a more specific insert to hold them in that area. Now its just a big pocket...as is the blue box shown (which I use for other counters I've used as life trackers).
Its 9 pages when printed. I can post all the pages on my BGG gallery if anyone is interested. I'll have to take some photos in action and put them up too.
Basically i stick my core game box in the middle of the play area...take out the oversized cards and set the ones i'm not using aside and it is a neat clean way to sort and store tokens.
You'll see there is a section designated for the new start of turn end of turn tokens. All the sections have been sized with the additional tokens from Shattered timelines kickstarter in mind.
Not nearly as exciting as the conversations going on about Shattered Timelines and Vengeance...but I thought I'd share.