nice idea 
 
 
This is something similar to what I made.  I used 2x4 for corner posts of the coop - have the floor 2 ft off the ground (yep split level) have 1/2 the floor with wire mesh and the other half contains the opening for the ramp for them to go below.  The lower end of mine is surrounded my wire mesh as is the bottom to keep anything from digging up or them digging out for that matter.  Will also help if I want to move them.  One one wall I have a 2x2 doorway for them to go in and out of and I have a door to close if I want to keep them out of the run.
 
I used old wooden fence section for one side of the upper coop, an old cupboard door for a door on one side along the back for access.  It wasn't big enough so I build another door to fold flat down.  This gives me 2 full sides to clean out the 1x1 wire mesh floor a lot easier.  On the 3'rd side I built the nesting box.  I only have 4 girls so they have 1 large box and seem to love it.  It's 12x24 - enough room for 2 boxes from what I've been told.  I have Barred Rocks who are now 23 weeks old.  The roof is made with 1x1's - I took extra pieces of wood flooring and put it all together, sealed it with some rubber roof coating that I had around and then painted the whole thing.  It's a bit odd looking but works great and keeps them safe, Raised 1 end up so the whole thing is slanted.  It has stood strong with the recent storms here in FL this past week.  The 4'th side is actually all hardware cloth - this design helps with ventilation here in FL - I have a door that I made out of another section of fencing so when the weather is going to storm or get cold I close it up for them.
 
The run is made with 1x1's and is 4x8 ft with 2 4x4 lids on top.  1 lid is partly covered with petal stripping to give them some shade and added protections.  It is only 2 ft high at the moment.  I have the whole thing covered on 3 sides with hardware cloth to keep them safe from other wild animals that may be around.  They do not free range at all at the moment, have more work to do in my yard to keep them safe from hawks, owls and a lake behind me with gators.  Gators can't get in my yard with the fencing that I  have so not a problem there.
 
I plan to raise the run up another 2 to 3 ft and add a door on one side so that I can access it better.  Right now I have to kneel down to lift the lid and put their feed or water in there or to clean it up.  I throw pine shavings into the run as well as under the coop and the girls love it.  They scratch around looking for bugs and such.  In the coop I also throw grass clippings in as well as veggie food scraps for them.  It keeps them busy always scratching things around looking for bugs and such and in a few months I'll be able to clean it all out and either use it in the garden or put it in the composter to further break it all down.
 
I do have a DIY composter made out of a plastic trash can that I put the coop cleanings in as well as what is under the coop when it needs cleaning out every few months.  I sprinkle DE all over the place for them to help keep things dry and control mites and such.  Have not noticed any smells at all and they have been in here since the end of October and we have had some days in the 80's.
 
Just thought I'd add my comments on here.