the meds DO work, you just need to find the right ones and the right dose and yes, it an be worse at these times. TBH my suggestion would be sort out the reflux first and get LO to sleep any way u can till he is rested again , then focus on independent sleep.
Sounds as tho u have many issues going on and boy do I know how that feels, hang in there and keep pestering your pead, babies shouldnt suffer unnecessarily, u're his mother, trust yuor instinct, if you think somethings not right well then it prob isnt.
Int he meantime try naps in stroller, car, swing, sling, whereever he seems comfortable. Have you considered a paci? this helps with the reflux