Oooh DrM that looks lovely 
I've had some browses through websites like "A Hutch Is Not Enough" (not because I have rabbits but getting inspiration for my guineas)
I think rabbits do get the hang of catdoors (but I couldn't find any that were straightforward slim fitting swinging ones online when I was looking. I gave uo because I don;t think the pigs would go for it . They aren't that bright)
Are you planning covers for the sides? Something like clear plastic that you can roll up ? I use a heavy industrial clear bag over one of the removeable windows (they're reinforced with bars and mesh+ chicken wire) . I peg it into the ground so they get air but if it rains, they're sheltered (they have a playhouse )
In the outer run, can you get a log that's rabbit safe to chew?
Digging box of soil if its on concrete?
Inside , will they use ramps ? I'm visualising a waist-height shelf with a full height barrier so they can't fall off (like a cot side) . Put a couple of hinges on so you can fold it down to clean and a couple of bolts to hold in place . (They won;t cost much and easy to fit)
Then the ramp going up the side , that'll give them an Under-the-Stairs hidey space 
You can put cardboard boxes under the shelf to play in. Maybe use the upper level as the haybox/bedroom as its off the floor.
I'd put a perspex screen on the bottom bit of the outer screen door so that the local cats didn't spray into the run
Lucky rabbits
looks great, now you just need to paint it bunny blue .