Landscaping inside run (shrubs/trees)...

Plant the biggest plants you can afford to plant. On top of the root ball cover them with hardware cloth before you cover them with dirt to prevent your girls from digging them up to dust in the fresh soil. This is what usually kills run plants not so much them eating them.

 

Why move the butterfly bush? Is it in a bad location? We have two butterfly bushes planted about 6 feet apart - it is our chickens' absolute favorite place to hang out in the afternoon. They each have their own little spot in the sedum that's planted underneath. One nice thing about butterfly bushes is that they grow faster than a lot of other shrubs. You could plant a variety of things, like a few butterfly bushes for faster shade/shelter, and some slower growing shrubs that will mature and fill out in a few years.

To keep the chickens from scratching them to death, you could surround the trees/shrubs with wire cages for a year or so until they are established. That'd keep your girls from scratching right underneath them, and then you can remove the cage and use it on another tree/shrub. DH made simple cages last year out of goat wire and a couple of those green metal stakes - worked great.

Besides shade/shelter for your girls, what characteristics do you want? Spring blossoms, fall color? Evergreens? How tall do you want them to get? Do you want edible fruit, like a serviceberry or chokecherry? Some crabapples are pretty little trees, but you have to deal with the dropped fruit (I don't know if the rotten fruit would make them sick or not - anybody know?). I'd make sure that whatever you do plant doesn't drop fruit or seeds that are toxic to chickens - any decent plant nursery should be able to tell you what's toxic to animals.

Does your yard have a sprinkler system, or need one for plants to survive? Do lilacs do well there? I love lilacs! They can be pruned up and are very hardy/drought tolerant. I wish we could get hydrangeas to grow here, but not even my Master Gardener neighbor can keep them alive.

My sister had heavies like yours, and they DID roost in her trees - one determined buff orp used to roost on her raingutters! So I'd assume if it's there, they'll try to fly up into it.