First let me say my heart goes out to you, your situation is one nobody should have to face
At the moment you are full of anger, hopelessness, frustration, blame and probably feel those against your self as well as the mother and the monster who so harmed your baby son.
It is not a good time to think and plan, so I would suggest you get proper help to deal with Child Protection Services. If you want to be the father of your kids and have them live with you, then get Legal Aid, or Community Legal Services to help you to prove you are of good character and are capable of looking after at least two of your children.
The third, your little by, might be an open question, he may in fact need specialist care long-term.
Do you get on well with the grandparents? If so a united front would be a big help, as would arrangements between you for problem days due to work.
AVOs are untested allegations, and so the above might be a path to consider.
It may be you have done this already, if so I apologize, if not then consider the matter.
Your own mental state and health do not sound good, and I'd be surprised if Griefline did not suggest you see your GP and explain the situation, it is not like someone passing away, it is an ongoing heart-break.
Try to be kind to yourself (that means food, exercise, sleep and distraction (books, movies, pets, whatever you happen to like), and if you have anyone who can give you support, family or freind, then seek it out. It is better when not trying to face all this alone.
I hope you come back and talk some more