This is my thought:
Go to the Knifeworks.com website and see their Maxpedition line. Click on "Bags & Cases". There are alot of bags with multi-pouches and individual storage areas that seem to be what you said you were looking for. Their prices are high but see if you can find a multi-pouch-organizer bag or three that'll suit you. Then search the myriad other sites selling Max[edition's gear for the best price. You can't hardly beat their bags and packs for storage and quality. I don't own any Maxpedition, but I've handled more than a few and I sure like their quality.