I’ll ask our head coach about the intent of the flat runs.
2) I would include them in your training logs. They won’t be helpful for training (well, maybe the descents for the impact), but you need to track them for the fatigue that they will contribute. If you use Training Peaks, their fatigue metrics will give you a good idea of this.
3) If it’s just a pull up you’re after, you won’t need 45-minute sessions, and I don’t think it’ll impact your run training. Check out the pull-up routine in our first book, Training for the New Alpinism.