OK, so after lots and lots of observation I have come to a few conclusions. I'd love to hear thoughts on them... First, I don't really believe the relux is the issue. It is pretty clear to us when he is having symptoms - he eats less at each bottle, he hiccups a lot more, he whines when he burps, etc. He does have flare ups sometimes, for a day or two at a time. That said, I am pretty convinced his NWs are related to us feeding him during the night hours because he ALWAYS wakes almost exactly an hour before we would feed him. For example, we DF between 10:15-10:45pm, and he ALWAYS wakes around 9:30pm. We had been feeding him around 2:30am (on the assumption that he was waking 4 hours after DF due to hunger), and he ALWAYS wakes starting at 1:30am. Finally, he ALWAYS wakes almost exactly at 6:00am (regardless of bedtime, which varies due to nap length, etc and regardless of NWs) and we feed him his AM bottle at 7am.
We have been gradually decreasing the amounts of the night feedings, and it has really improved the consistency of his consumption of daytime bottles. When we were giving a full feeding in the wee hours, he would only take 2 oz or so at 7am. As we have weaned it down he now takes his full 6oz feeding at 7am. He had a few nights in the past week when he would wake at 1:30 and we would shh him, then he would not wake for the feeding at 2:30am (sleeping til the 6am wake), so we have decided to eliminate that 2:30am feeding. If this is successful, we will then move to eliminate the DF as well.
DS is a large baby (99th percentile for height and weight) born on his due date. He is nearly 5 months old now, perhaps a little early to wean the NFs but we CANNOT keep living like this. He wakes our DD (almost 2) up with each waking, and she was sleeping very well (11 hours/night) for the past year or more and now her sleep is a mess too. Something has got to give! He is a very happy little guy, very pleasant and napping great during the day. If it weren't for the NWs I'd say he was an angel/textbook baby.