Thank you everyone for all of your thoughts and advice. I am going to trying to answer each question and thought, so this may be a bit jumbled.
londonmama, thank you for all of the links you have provided (including the ones on the other thread). You have stuck with me for a very long time through this, and been very supportive and helpful. I am always willing to listen to anything you have to say.
Vikki, Dylan's mommy! thank you as well for the link.
brenda2, when you were having NWs, how long were they? A few minutes, or hours long?
Restarting the reflux meds may be something that we have to do. I have not been able to get an appointment with the paed until the middle of May, so that will not be an option until then.
We are not seeing an allergist. There is not one close to us, as we live in a rural area. All we are seeing is a GP and paed.
I have been keeping food and sleep diaries since about 3 months old. The sleep diaries were started because at around 2 months we were having nap issues. Then at 3 months he stopped STTN, and I was a bit concerned. The food diaries started because I knew he was not having as much as he should have been having to eat/drink, but wanted to see just how much. Then I continued because I thought it would be fun to keep a log of his first foods as a keepsake for when he grew older. The sleep problems continued, and I thought perhaps there was a correlation with the food. I have just continued since then. They just give a list of the general foods he eats and amounts, not each specific ingredient.
DS had a blood test about 3 months ago for milk, soy, egg whites, and fish, and I'm not sure if there was more. That is how the MPI was confirmed. He is still getting some amounts of milk proteins. Very little I am sure, but I haven't kept track of exactly how much. I was told by his doctor to keep him on trace amounts of milk proteins, so that his body would hopefully become used to them from repeated exposure, and he would outgrow the MPI. I was told to cut out obvious sources, such as milk (and formula), yogurt, and cheese. Since he was diagnosed MPI, he has been on a soy formula. We did have a good 2 week period of sleep at the end of Jan/beginning of Feb, where he would wake up 2-4 times a night and put himself back to sleep almost every time. I think I was only in his room twice in one week, which is really good for him. At the time he was only drinking 4-8oz of milk formula a day, so I was sure taking out so much of the milk proteins would help, but it hasn't seemed to make a difference.
I have been giving Tylenol and some camilia for the teeth, but have been avoiding Motrin and Advil. The Motrin and Advil seemed to help sometimes, and other times they just seemed to make his stomach hurt and make things worse, so I was giving them very infrequently when londonmama recommended I stop completely, and I haven't given any since.
The amount of formula he has before bedtime does not seem to affect his night at all. Some nights he only has 1 oz, other nights 9, and it doesn't seem to matter which he has had whether we have a good night or bad.
I have been sticking to the 7 pm bedtime because I have been so inconsistent for so long with his times. Because we were going back and forth between 2 naps and 1 for so long, his day was all over the place, and his bedtime was varying by hours. So I guess I have just tried to be consistent with this. I have tried for a 6:30 bedtime a couple of times, but he still has not fallen asleep until 7 or 7:30. I am very afraid to put him down earlier, as he tends to do a 10 or 11 hour long night, even with all of the NWs. A 7pm bedtime results in a 5 or 6am wake-up, so I am afraid to go earlier and end up with a 4 am wake-up, especially because there are nights I don't get to bed until 2 or 3.
He was put down to sleep independently until about 4 months old. If he had problems falling asleep, I would rub his back or pat his bum. The sleep got worse and worse, and by around 7 months we APed to sleep all the time. He was rocked for quite awhile, and now is to the point that we just hold him until he gets drowsy, then put him in his crib. When he has a NW, I listen to see what kind of cry it is. A light cry he will likely put himself back to sleep. Screaming, I go in and lay him back down if he is standing or sitting. I will try that a few times, and leave my hand on his shoulder if he seems to need it. If he keeps sitting up or screaming, I will pick him up and hold him until he gets drowsy again. He has had only 2 night feeds in the last (about) 8 months. 1 during the night a couple of months ago, but he was up for a couple of hours after that, so that was ruled out as a reason for some of the NWs. Another was for an EW, to see if he would go back to sleep (which he didn't) so I haven't tried since.
I think I am saying it poorly, but I do think the AP is part of the problem. There are some times when he cries that I am pretty sure he just wants me. I just don't think it is the entire problem. And I personally feel that it is unfair to try and sleep train if he is in pain. I definitely never thought I would still be helping my almost 17 month old to fall asleep. I'm just not sure what else to do. I feel that there is something else wrong, but it is hard to get help from anyone once they hear about the AP. But I feel like I can't wean the AP until I figure out why he is in pain and waking up screaming so often. So I feel like I am stuck in a loop, and I'm not sure how to get out.
I have started up another thread on the food allergy board to see if I can get some more ideas
http://babywhispererforums.com/index.php?topic=169939.msg1903606#msg1903606Thanks for all of the replies!