So, the original insert had 2 problems for me: 

1. With 110 micron card sleeves, both expansions and few promo cards (3 exactly) around 15 cards won't fit into Imperium deck holders. And even with those few cards out overall fit was uncomfortably tight. Thankfully I managed to slightly change angle cards holds in this tray which allowed me to increase space for cards without changing outer dimensions. Imperium logo was destroyed in process though.
2. I've printed first player marker in form of Worm and influence tokens, also painted both. Soooo, I decided to fit them in this insert without much rework. So, I cutted conflict deck holder so it fits at the right side of the insert without those unnecessary “Wings”. After that I created from scratch "bits" tray to fit all of those extra components nicely and organized as well. Now its consist of outer part, which needed to keep all those boards nice right whey they are belongs and inner part, which consists game pieces and can be pulled out separately. Fingers hook also serves as a stand for the boards on top of it.

All other files remains unchanged.

If you care about vertical storage or box trasportations @Kniephaus created cover for token storage and also added place for 2 more influence tokens (if you gonna use it with Uprising): Vertical Storage Cover for "Dune imperium Organizer alteration"

P.S. Also uploaded my version of resources trays. Those fingers cutouts not needed IMO as you can easily grab them by inner walls. And getting rid of those cutouts making middle slot normal instead of being squished and inconvenient.

P.P.S. Outer file is totally optional. I found myself liking how the game stored without it, so I'm not gonna print it at all.