1) Workout starts after warming up. You do not need to warm up for every exercise as outlined in the directions. Once you warm up chest for your first exercise, you do not need to warm it up on your second or third exercise. These workouts are extremely short and there is no reason you shouldn't be able to finish them within 30-45 minutes. Keep your rest intervals 45-60 seconds and DO NOT warm up for every individual lift.
2) You are overthinking this. If you are using a secondary muscle during a lift, it is already warmed up, thus there is no reason to start from 0 and warm it up again
3) I quickly warm up abs b/c mine cramp up horribly if i don't when I weighted situps
4)Waxy maize + aminos immediately after my lift. 20 minutes I pound a whey shake. 30 minutes to an hour later, then a PWO meal. This is highly recommended