Hello I saw this thread and the situation pretty much mirrored mine two months ago so I thought I would chime in and see if I could help
My LO had the exact reflux issues as yours. He is now almost 8 months now but the first 6 months were a trainwreck! He also had the same feed times as well, NF at 1ish and another at 5:30ish, I was also confused on how to iron things out but here is what I did.
I took him to see a gastro and he put him on Prevacid which worked wonders. The Zantac did nothing, but the Prevacid certainly helped. I also started feeding him solids and, same as you, he had intolerances and I stopped, but I still continued his rice cereal with pear juice. It was very gentle and did not bother him at all. He ate this at breakfast and dinner times (along with a bottle) and had a bottle for lunch. Now he eats pears, carrots, apples, bananas, and sweet potato just fine and has them at 7:30am, 12, 4:30. This is always followed by a bottle. Also, try cutting his bottle back by .5oz, this really helped him too.
When he was still waking for his 1am and 5:30am bottles I would give him full bottles. But eventually I had to cut out the 5:30am bottle. Do this first. I know that sleep is important, trust me I lose my mind without it, but if he wakes at 5:30 leave him in his crib unless he starts crying. My LO learned to either play by himself or nod back off to sleep. Do you use a paci? I like to surround him with them incase he wakes and wants to go back to sleep and needs a little help. So, he may wake earlier but this will change soon.
The most important factor in him getting a good nights sleep is controlling the reflux. Nothing can really change if he is uncomfortable. This is something I was forced to learn. I was always trying to implement EASY and getting frustrated that nothing was going right. Once he started sitting up all the time, his reflux was much better.
My LO also did the phantom SSTN! Once every couple of weeks he would and it was incredible. But, the rest of the time, I kid you not, he was up ALL NIGHT EVERY 45 MINUTES with reflux issues.
I think he is too young for a 3hr A time unless he is almost there already. My LO is not up to 3 hours of A time yet and I am still struggling with dropping the catnap.
Once the 5:30am feeding is out of the way, he starts eating some solids, starts sitting up a bunch more and the reflux is under control, I think he will start sleeping right past that 1am bottle. It wasn't until a couple weeks ago that my LO stopped that feeding. We only gave it too him if he woke for it. If he keeps waking looking for that bottle, I would say give it to him. But try to settle him first and see if that works.
I hope this helps!