Hi Dianne,
Your little one sounds so much like mine was….wow. Well, I can tell you we had identical nights for a very very long time. I’m really sorry you are going through this. It will get better. Just remember that. If nothing else, age and size and time itself will help things get better. Not to sound scary, but we ended up finding out so much through testing and time. My son is now two years four months old and his nights have dramatically improved and for the first time here– I can’t even believe I’m saying this– his nights seem to be nearly as “normal” as many other children his age. (I hope I am not struck by lightning for writing this! haha).
Have you done any testing yet…just curious. I’ll share some of our background so you know where I’m coming from– my son was also a happy camper during the day for the most part after about 11 mos of age (miserable before 11 mos in general), but suffered from severe painful night wakings until about 18 mos of age. I also bfed, I was also on a restricted diet, he was also MSPI, we discovered a hiatal hernia in his endoscopy. The ph probe showed he refluxed an average of every ten minutes day and night, only it seemed the night time ones bothered him much more than the day ones. He has been on 40mg of Zegerid every day since about 11 months of age. We also use probiotics. I also used aloe vera juice for a while. When things were in the process of really getting better– around age 17 mos– we also saw our family chiropractor who specializes in babies several times for adjustments for him– it really helped. I got to where I had exhausted western medicine (I even asked our ped gi if this was the case and he agreed)– we’d been turned down for the fundo surgery as bad, but not a bad enough case– so that’s when we actively began looking into other options, including aloe vera, probiotics and safe chiropractic. We also now see an allergist and finally got on board with a diet that works for him. I think a lot of his problems were reflux complicated with multiple food intolerances– as he’s tested negative for all formal food allergies. Our allergist is great and we do food trials once every six months now that he’s over age two.
Our specialists and ped both said that pain at night is more noticable than pain during the day….babies and adults can be distracted from pain a lot more easily during the day than at night. I completely agree with this after seeing my son. It was just so hard to believe unless you were there to see the difference in him– so I really know what you mean!
So, I now feel that he has suffered from both upper and lower gi discomfort all this time. It wasn’t until we removed all gluten and wheat products from our diets (while I was bfeeding) and from his diet now, that things have turned a huge corner (this was around 17-18 mos). In case you are unfamiliar, gluten is the stuff that makes wheat bread dough elastic-y, it’s something in many grains that helps them to stick together. It gives a wonderful consistancy to most bread flours, but isn’t in rice and a few other grains. He has tested negative for celiac disease– so it seems all his food problems are protein intolerances.
Lucas also was a very fitful sleeper, and I’ll save some space here just saying that he sounds a lot like your son and you can imagine how terrible it was not to sleep for 17 mos. 
At 17 mos I was desperate enough to try removing gluten from our diets and things very gradually improved from there. He still cna’t have citrus or tomato or other really acidic things, and also doesn’t have dairy/soy/beef/and gluten products. He has a very healthy diet and is on track for weight and height. He is not suffering from not having these foods and we’ve found very good options for him in terms of replacement foods. I was on the diet as well, so I had to find things that tasted good and satified my adult palate.
When he was between 8-10 mos I stopped all solid foods for him and only nursed so I was more in control of all the variables….but I consciously decided I couldn’t handle removing wheat and gluten from our diets. It was overwhelming, I was alrealy not eating dairy and soy and beef and all the classic reflux inducing acidic things. I seriously thought I would starve. I was mentally unable to cope with removing yet another large component in my diet and finding yet another new way to eat. In hindsight, I should have taken the plunge and just begged my mother to visit or something, so I could have help to figure out how and what to eat. (In the beginning, it takes a lot of time reading labels in grocery stores, etc.)
Knowing what I know and hearing your description of your scenario, here are some thoughts.
If you aren’t already seeing a specialist, you really should, a pediatric gastroenterologist. They just know so much more than the average ped, and they can do testing if need be, etc. etc.
Have you done the formal elimination diet, where you begin with rice and potatoes and move on from there? Did you notice any differences with the classic food allergens like eggs, fish, wheat, etc.? How much is he nursing vs. Neocate? Do you find that he seems more comfortalbe after having his neocate than after nursing…or are there any correlations with those two? How much is he eating solids? It sounds like his zegerid is a very LOW dose to me….I hear what you’re saying about not wanting to have the horrible night you did when the zegerid was higher, but would you be willing to experiment with the dosages that are recommended on marci kids — or give it antoher shot? I would look into these:
–Probiotics are bacteria that encourage a healthy enrironment in the gi tract, they are safe, and they make a powder for babies that you can give via syringe. They make a tablet for kids who have teeth and can chew. It helped us a lot.
–Aloe vera is liquid, can ben given via syringe like meds and is very soothing and can help relieve pain as well.
You might just think about taking out wheat or go whole hog and do gluten to see what happens.
Teething for us was a complete nightmare, and looking back whenever things were at their worst, it was the teeth. We gave a dr. approved cocktail of hyland’s teething tablets, children’s benadryl, children’s motrin, and I can’t remember what else. It was so seriously bad that I would rather have just gotten him dentures. I’m serious! 
I think I’m just rambling now, please write back with your thoughts. I know it’s a lot to take in. Ask away if you are wondering about what to eat without gluten, etc. Also, I can give you brand names of the aloe and probiotics. I’m just so amazed to hear about someone who sounds so much like our situation! Hang in there!!
