Hey there,
Forgive me if I have missed this but how old is your baby boy now?
Is the reflux under control? Is he on any meds, or thickeners etc for it?
I have had two boys with silent reflux and one also has food intolerances and I can promise you these bad habits we create, they can be undone

when our babies are in discomfort we just have to survive, we just have to get through the bad patch best we can. So try not to worry about the AP, you can't ST a baby in pain anyway so you may as well find what works and do that (we even had a recliner in my DS2s room)
Does he respond to swaddling?
How long does he need to have no baby wearing or soother?
Sorry so many Qs and lots of hugs x