I know you know your baby and what works for him. Sounds like you have thing under control, and you are right, if he is crate trained and is comfortable there, then that is the best place for him.
I don't crate train so that is why I offered the hold in lap alternative. I have sat up many a night with dogs, cats, horses, etc.
Have you felt his sweet little tummy to see if he might have any discomfort, like maybe he might be constipated? Could he have gotten a bug bite?
Good luck to you, Cherry, hope all goes well tonight and your little guy gets to feeling better real soon. Isn't it a grand thing that we have YT -- you know that someone will be there 24/7...