As well as Werckmann organizer boxes stack onto each other, it's tedious when you need the one of the bottom - so I wanted to have a sturdy shelf for them where I can just take the one that I want. I may have gotten a bit overboard with the sturdiness, but well, at least I know it will be able to carry everything I put into it :)

shelf.
The boxes get loaded sideways so I don't waste any depth on the larger shelf where it sits.
You can stack as many stories onto another as you need - the stories get screwed together, but this is more of an optional step (they have locators so they don't disengage, and the weight of filled organizer boxes should keep them down); I still recommend it though.
Two halfs get connected by two threaded rods, little bridges with sloped ends get onto these so the organizer boxes don't get damaged by the thread and don't fall out as easily.

I agree that threaded rod isn't the most elegant solution, but they are dirt cheap (88 cents for 100cm), cut fast, and make the shelf very sturdy.
While you can use only shelf pieces to stack on top of each other, I also made bottom and top pieces which lack the additional locators/screw terminals; these are purely cosmetic though, I found it a bit nicer. As the cut ends of the threaded rods don't look so pleasing on the sides, I decided to provide some "plugs" you can just put on top (see photos), just to make it look a bit more slick.

BOM - what you need.
per story you need:

• 2x 194mm M5 threaded rod
• 4x 10mm M5 countersunk screw (optional if you don't want to screw the stories together)
• 12x M5 nut (minus 4 if you don't want to screw the stories together)

Yes, it's a lot of M5 nuts; but as a pack of 100 costs around 3€, I didn't mind.

assembly.
It's pretty simple - you screw two M5 nuts onto the ends of the threaded rod, and push these into the compartments on the inside of the shelf pieces. Then you screw on another M5 screw from the outside to sandwich the printed part between these; see the photos for some detail shots.
The distance between the two halfes is meant to be 170mm; I added some distancers which help tremendously in getting this setup properly.
Two stories are connected by four countersunk M5 screws and nuts; just push the nuts into their compartments on the inside, place two stories on top of each other, and secure with the screws. Push the bridges onto the threaded rod; I distanced them around 44mm from the sides (I used some large M15 washer that sat on my table, no idea where that came from).

printing advice.
Due to the honeycomb the parts don't print fast, but are very sturdy. The provided profile has all parts integrated, as well as the very rudimentary colour swap (just delete the 2nd filament in case you don't want that). The shelf pieces should be printed with a brim; some parts need support, pretty easy to remove in PLA though. Generally I recommend PLA because it's plenty strong as well as stiff, also a lot cheaper.