always I work in Early Years education, and have spent many years talking to parents about boundaries! It is not about being soft or hard on him - you might find it helpful to think about boundaries not as you forcing your will/opinion on him, but as you providing a physical and emotional space where he knows he is safe.
Decision making is absolutely exhausting for small children (for adults too...). If children feel that they are responsible for making all the decisions in their lives, they get overwhelmed, and it can make them feel very anxious. This doesn't mean that we should take away their autonomy, and it doesn't mean that we should force or manhandle them into distressing situations. But it does mean that we, as adults, explicitly take responsibility for certain things.
So with the medication, for example, you might want to say to DS something along the lines of 'your brain is really struggling at the moment because it hasn't had enough rest. You need to get a good night's sleep, and this medicine will make sure that you can do that. I know that you're worried about it tasting nasty, so I'm going to squirt the medicine straight into the back of your mouth so you can't taste it, and here is [something delicious] to make sure that you can't taste it afterwards. Ready? 1, 2, 3 [do whatever needs to be done to get it into him]. Done! Amazing. Here's your xxx.
His feelings are acknowledged, but he doesn't have to make a decision about and take responsibility for making himself do something that he doesn't want to.
Hope that makes some kind of sense!