I haven't read the whole thread yet, it may have already been suggested.
With a shed, you can do something like dog breeders do. You can have individual pens/coops on either side of the door - leaving a walk space from the door to the wall opposite of the door. Then on either side have either each be one big set up with a run off of each or divided into smaller sections. Put nest boxes so you can access them from your walk/aisle way. Make a door into each section that you can go into to deal with cleaning, watering, feeding. Make a pop door on the outside wall to allow chickens into their run.
The full size of your shed will determine how many chickens and ultimately how many pens you can have.
I don't have a set up like this, have seen several. If needed, I can draw a picture (won't be very good, not a good architecture drawer). Or you can google and probably find pictures. I can't remember if there are any pictured on the coops area of BYC or not.