Our coop and part of the run are in our barn and like you, we used dog kennel panels to make the run. 2/3s of the run is outside the barn giving the chickens a grassy area to do their thing in. The only thing we have done differently then your plans is we have ran a hot wire approximately 6 inches off the ground all around the parameter to prevent anything digging under and hopefully climbing the fencing. We used bird netting over the top mainly to keep birds of prey (which we have an abundance of) from swooping down from above. We aren't too worried about break ins during the day because one of our dogs is usually outside much of the day and at night the birds are locked up in their coop which is made of solid oak and metal siding. Any raccoon would have to bring its own sawzall and metal cutters it is that desperate for a chicken dinner.
I would suggest securing the bottom of the panels against dig ins by either putting down wire or using, like we did, an electric wire around the entire barn. Yes, it's a bit awkward and yes you will probably get yourself zapped at least once (it's one of those things that you only do once and then never again because it is too unpleasant) but it will give you peace of mind where your flock is concerned.
