Hi D.,
Funny my son is called Zachary and he's the same age as your son...small world. Sorry to hear of the problems with Alyssa, my son was diagnosed with Reflux just a few weeks after been born. He was fine while I breast fed but we had problems and we had to switch to formula and take Zantac. At first they thought it was colic as he didn't spit up but as it was always after he fed he screamed they decided it was Reflux. We found that the Zantac really helped we tried a few formula and ended up with Nutramigian, its expensive but pre-digested so its way easier on them.
I found he slept much better when sat upright, he spent hours in his swing. I put a towel under one end of his matress so he was never really flat.
If he went too long without feeding he was in pain and if he got too full so I fed him little amounts often. The Nutramigan digest quickly so he had to fed every few hours. He was only 3 months or so when we started putting cereal in his bottle, which also helps and once he was on solids much better still.
We were told he would outgrow it by 6 month, he didn't, then 12 months, he didn't, then 18 months, he didn't. Eventually at 2 we stopped the Zantac and he's not had problems since. PTL.
I would try the Zantac again, it takes a while to help them I believe, try giving it through the day if it bothers her at night. I believe you can give it all in one dose rather than split over two. Then again I remember the Doc saying it can feel like its burning some babies so splitting its best.
Good luck and try not to worry, they pick up on your feelings too.