Formula/Reflux/Alimentrium Questions...

Its been a  roguh few days & I have cried so many times today thinking I am a bad mom who cant figure out what is wrong with her child!!

My Dr is trying at this point to determine if LO is dealing with a relfux issues, food allergry, congestion, etc. First we thought he had a cold, but its been 1 week, no fever or coughing just congested still, not in lungs (no wheezing) just in nose. At yesterday visit, Dr said she thinks it may be a formula allergy and switched us from enfamil gentlease to similac Alimentrium. She said this is why he could be congested/lethargic & so fussy lately. She also has us using gripe water x3 a day.  I switched yesterday & she said I should see a signifigance difference in 48 hrs. If not, I need to bring him back in & we need to start exploring diff. routes like reflux and see a GI specialist & get blood drawn, etc. My LO seems to be doing much better today.. is actually eating without pushing the bottle out of his mouth & arching his back... he took two HUGE poops...he actually will eat & then fall right back to sleep so I am guessing he is comfortable. My concern is that twice today he woke himself up gagging/choking which turned into a cough and crying. I burp him as best i can before I lay him down and usually hold him for a good 10 mins.He also still doesnt seem to be comfortable on his back only his tummy. I am thinking there still may be an issue here... possibly reflux. Sound familar? Should I be seeing a big difference right away? He seems less fussy but last night was still rough (granted it has only been 1 day on the new F)