Ah! Now we can use their habits to either shoot them or trap them! Your choice - .22 rifle or a live trap.
If you wish to shoot them, set yourself up at sunrise with your loaded weapon. Or at dusk, two hours before sunset. Those periods are their highest activity.
If you wish to trap them because you can't bear to kill an animal with big soft brown eyes and a fluffy tail, although they are rodents every bit as disgusting as rats, (sorry, my bad attitude comes with being fed up with them), set the trap at their point of entry into your run. Bait it with whole dried corn or peanuts. But you need to remove all the chicken food from the run or they will keep focusing on what they've been after all this time, which is their lazy way to easily obtain food to hoard.
These squirrels are compulsive hoarders. They will gather huge amounts of food, far more than they will ever consume. It's their reason for existence, their fun and joy, their compulsive habit. This is why putting out rodent bait will not work. They just stash it in their many food caches.
But if you trap the squirrels, and you don't wish to kill them, you will need to relocate them in the next county. Or state. They are persistent about returning, and will cover many miles if they have to. Your local county laws may prohibit relocating them to keep disease under control, so best to check on that.