HopefullyI can explain this thoroughly. I'm not sure where to even start.
My son is 3.5 months old (4 months on the 20th of this month) and he is on a 3-hour EASY schedule that almost always follows the one below:
8:00 - E
9:00 - S
11:00 - E
12:15 - S
2:00 - E
3:15 -S
5:00 - E
6:00 - Cat nap
8:00 - E and then diaper and bed
He is on medication for reflux and I am also on a no dairy, no soy diet because he is sensitive to both and I'm nursing. During the day, we have finally gotten to a point where he takes nearly perfect naps. He ALWAYS (no exaggeration) goes to sleep awake for naps and bedtimes and is EXTREMELY easy to put down. He currently takes 3 naps that vary in length from 1:15 min to 2 hours , plus the 40 minute catnap. During the day, he takes the binky during the wind down routine (which lasts about 5 min tops) and then, once in his bed, doesn't care at all whether it stays in his mouth or not. Either way he will go to sleep. During the day, I never have to re-insert the binky.(Also---he LOVES to suck his thumb or fingers, but is swaddled when he sleeps so he can't use it to self-soothe. I've tried leaving one hand out to see if he'll start using it but he just cries until I swaddle the hand back down and then goes to sleep.)
Here is the problem:
He used to go to bed after the 8:00 feeding and sleep until 1 or 2 without waking, but for the past few weeks he has been waking 3-4 times before I feed him around 2:00am. After weeks of trying to get him to take a dream feed I decided to stop forcing that. He would never wake up for it, and when I forced it, it usually caused more night wakings. Currently, our nights look like this:
8:30: Bedtime
Between 10:30-2:00: 3-4 wakings. I put the binky in his mouth and he goes right back to sleep. Never cares that he isn't eating.
Approximately 2:00am: Feed and sleeps for 3-3.5 hours
Approximately 5:30am: Wakes.
NOW THE REAL PROBLEM BEGINS...
Between 5:30 and 8:00 he wakes EVERY 20 or so minutes wanting the binky back (or at least waking and crying seemingly wanting the binky)
I'm so baffled by this because during the day he has virtually no sleep issues. Any advice or input would be greatly appreciated. I'm not sure if I should wean him off the binky completely or what to do? I am terrified of trying to wean him from it and having that affect his napping since it is going so well and he doesn't wake to have it re-inserted during the day.
Okay, I think I have included everything. Please help! I want to have a good plan for tonight! I'm exhausted!

--Oh and I forgot to add that he always sleeps in his crib in his own room. No nursing to sleep, or rocking or swinging etc.