I have a set up like this. It works really well for my two. I will try and get you a picture of the full set up tomorrow (it's night time here now)
Mine is a six foot by 4 foot shed, attached to a run of the same size. There is a bolt hole in the side of the shed that has a sliding door on runners if you know what I mean?
I have put down an anti slip lino on the floor which makes it easier to clean up any mess that has found it's way out of the litter tray. The extra height of a shed makes cleaning and interacting with your rabbits much easier. It is a life saver when the rain and snow comes as you don't have to be outside in the bad weather and can sit in the shed and be cozy
Some people mesh a couple of feet up the inside shed walls to prevent chewing, but I have not had to do that so far as my little ones are not chewers. On the main door I have placed a mesh barrier that is tall enough to stop the rabbits running out of the door when I open it but short enough for me to be able to climb over easily. I have also attached hanging toys to this mesh barrier so it ascts as an extra plaything
My run is not a "walk in run, it's about 3 foot tall, but it is predator proof (to many cats, foxes, ferrets, buzzards etc here for it to work otherwise) and so the rabbits have twenty four hour unrestricted access to the run. The only time they are shut inside is when I am cleaning the floor (the run is on concrete to prevent ferrets and foxes digging their way in, or rabbits digging their way out)
Anyway I will post some pictures for you tomorrow so I can show you how we did the holes and what it looks like