Dude. I know you've avoided this for as long as you can. Mate either get a lawyer or book into mediation. You need to sort out custody. No ifs, no buts. She won't listen to you and will only do what she wants and it won't be to your benefit. Ask her how the kids are getting upset. I have a friend in a similar situation but his kids are way younger. He's agreed not to have them during the week but won't agree to it being legal. Stand up guy with his kids interest at heart.
As for your S's medication? Nah, unless you hear it directly from the doctor then don't change anything. You can phone his Doctor from work and ask for clarification of how his meds are to be administered. Just a concerned father looking out for the best interest of his child.
I still think you're holding onto that rope. Perhaps that's something to think about.
Peace buddy.
Me:43 Her:42 M:14 S:9 EA started 2014/03 (or there abouts) PA started 2014/05/30 BD:2014/11/05 I left 2015/10/01 I returned 2015/05/02 She left 2015/06/10 OM still on the go.