Thank you all for comments and suggestions!
Yes, the inside beams are a problem so I thought about stapling foam padding around the beams and covering the foam with fabric, to give some protection when you misjudge and raise up too soon
Since we are going to have to trench near the run I am going to dig down and bury wire around the house, DH thinks the way he flushed the metal to the ground nothing can get under it but yes they can if they are determined enough too
the kennel that was given to us is 10' tall panels, so I have been playing around with how to get the most out of each piece, some of the panels will be roof for the run, we are also going to wrap the top of the run with chicken wire to deter large flying predators and to keep the hens in
Partly covered run, sorry I couldn't get the best shot of it but this is how I am going to lay the extra panels over the run then put a layer of wire over the panels
The kennel is beat up and missing some links so we are securing all the places with wire
When I get it all the way I like it I will try to post better pictures of the top of the run, we are putting the floor in today and yay!