The idea for the barbell is essentially to be light enough to move easily. Because of this, it should make those runs hurt. As with anything we do, intensity is the key to any progress or good workout. So if dropping the barbell is something you see doing at any point in this workout, scale it down. The weight on the barbell doesn't matter, it's how well your body moves whatever weight it is. Today, it needs to be easily. Breathe on those runs, and pick up that bar as soon as you get in. Run and squat. Easy.