First, congrats on the purge and re-org!
I have some weird sets like that.
I don't store by company-I store by product and then category.
The ones with stencils that are 6 x 6, I put it in the same storage pocket for a 6 x 6 and they have their own box for mixed product sets.
If they don't fit in that facing forward,, they get a larger pocket and go sideways in the same box. (So far I dont have a lot of those odd sets) If I get more, then the regular sized pockets will switch to facing to the side instead of forward. I hope that makes sense. aka I have to pull the box out fully and turn it sideways to now be looking at the pockets full on. (I already have a few boxes like that for oversized sets like say the monthly Hero)
So they are in their own "weirdo" box lol.
Another choice...if you store by brand and not product, and you are in a box, and it is too big, you might be able to pop it on the side? I have some large stencils items like that. Like scrapjenny said, pick the item you remember the set for most for which box.
OR you could have a dedicated standard binder for the weirdos....and use full page pockets with a lightweight piece of cardboard with a piece of magnet to hold a die in place. Put the whole set in there.
Let us know what you decide on! Good luck!