My storage solution involves putting foam core fittings into the base game and intrigue boxes, to make three columns of cards in each box (after taking the plastic fittings out). Until Renaissance, I was using the sixth column for mats and tokens. I don't really have a storage solution for those anymore (hmm... maybe the Alchemy box because it's smaller), but now the Renaissance cards fit in. I use index cards cut in half which stick up just above the cards as labels (handwritten).
This doesn't include randomizer cards or blank cards or the extra set of base cards I got from 1E Intrigue, but it does include extra setup things excluding the mats and tokens, like Events, Landmarks, Projects, Ruins, Boons, Hexes, etc.