Sweet! Lovely kayak. One of my favorite places to be is in my kayak, especially when the mist is rising off the lake in the morning.
Does the fence wrap around the long side and the back of the building? How many birds are you hoping to house? I'm assuming the fence runs parallel to the long wall? Are you planning to cut in a egg nest access door? I like aart's idea about putting a roof extension over at least part of the run. If drainage is an issue, you might want to install a gutter system along with a drainage ditch to keep the water away from the coop/run. Your skirt will be the most important safety feature. I also suggest that you put one floor level vent, and put some high level vents, aiming for 8 - 16 s.f. of ventilation. (Your windows count as part of that total. If drainage is not an issue, and you put in a rat proof skirt, a soil floor would be great for DLM. You could coat existing framing and siding with black jack to water proof them. Make sure the shed is structurally sound before putting a lot of effort into the re-do! Looks like a fun project.