I am thinking of doing a three tier setup like yours. Here is what I was thinking of doing. Get a small pouch that can attach with ALICE clips to the outside of the Fatboy. Either the Maxpedition M1 or M5 waistpack would probably work well. There are also many other pouches out there if you look. Put your level 1 kit in the small pouch, and attach it to the Fatboy. Then put your level 2 kit in your backpack in easy reach.

Here's how it would work. When you just have your EDC + Fatboy, you have your level 1 FAK in an external pouch that is easy to get too. Then if your are moving up to EDC + Fatboy + Backpack simply take the pouch off the Fatboy and put it on the outside of your Backpack.

Now you have both FAKs in easy reach and you can use contents from both very easily. I know this isn't a perfect solution for you because you wanted to use hard cases. This was just an idea I had and thought I might share it with you.