OK, lots going on then. First off, some ((((hugs)))). Let's see what we can figure out here.
If you suspect reflux, there's some good info on it here:
Reflux 101 - General reflux information as well as the forum here:
Colic, Reflux, & Crying . The ladies there are very knowledgeable about reflux and can be very helpful.
Next off, his schedule. At 13 weeks, we'd expect that he'd really only be able to stay awake for about an hour and 20-30 minutes at a time (you can look here:
Average A times and "Is my baby ready to increase A time?" for some more info on that). He's got some really long awake times going there, so I'm wondering if he's just overtired and all that overtiredness is piling on top of each other during the day and causing all of your night wakings. There are some sample EASYs here that might help you get a better idea of what you might aim for:
chronological EASY samples, 0-3 months .
It looks like he's on track for a 6-6 day -- so you might want to try something like this:
6 - awake/bottle
7:30 -- winddown, in bed to sleep -- at that point, you would work on trying to get him to settle in his cot by using pat/shush --
Pat/shush for babies under 3 months old and he'll hopefully sleep until somewhere around 9 where you would start the cycle all over again.
I will say that the more I look at your post, the more I think you are right about either a food allergy or reflux -- we've got a food allergy forum as well that might help you out:
Food Allergies -- the stuffiness, constipation, and poor sleep all point to that.
And finally, take care of yourself as well -- is there someone at home who is helping you get some sleep at night? Post in the PND forum if you feel like you need some extra support, there are always some hugs and support around here:
Post Partum Depression 
