I understand not wanting to be too aggressive when he is sick.
When he is feeling better and has had a couple of good night sleeps (as much as possible) and on a night where you don't have too much going on the next day, try putting him in his crib after feeding him a decent meal and giving him a nice warm bath.
If you haven't tried, prop the mattress up a little with blankets (under the mattress) to create a slight incline. This might help with any reflux.
We have also used very soothing music and a night light to help create a nice environment to help our daughter self-soothe and fall back asleep.
We've also recognized that the temperature in her room plays a role.
It is always a guessing game and then once you get it, they change the rules.
Talk to you doctor, it can't hurt.
Good luck to you!!!