I'm having almost identical problems with my five month old daughter! She also spits up a lot, but Zantac wasn't good for us. We gave up the binkie because she started waking every time it fell out of her mouth & we could see that it was becoming a prop. Our daily routine is also very similar to yours, although my daughter still takes a third nap.
When my daughter wakes in the middle of the night, her crying escalates, too. We've been doing shh/pat because the PU/PD technique seems to agitate her quite a lot (she's Spirited). We've been doing this for a couple of weeks now and her night wakings are becoming later and later. She has a DF at about 11:00. Then she usually sleeps until about 4 AM. From 4 AM until about 6:20 she fusses and dozes, while I shh/pat (and lie on the floor of her room). She almost always dozes by 6:30 and I have to wake her at 7 AM to begin our day. My hope is that, this 4 AM waking will become later and later as she learns to soothe herself back to sleep during the night.
I think it was Teezee who posted that "babies cry, they are supposed to." In accepting that, I've noticed that my daughter seems to simply need a little "cry time" before going to sleep. Nothing is wrong and she isn't really upset. Of course, I have trouble hearing her cry, so I lie on the floor by her crib and shh/pat if the crying doesn't begin to wind down eventually. I think she is learning how to settle herself. This has been EXHAUSTING, but I think she is sleeping longer and longer at night and will, hopefully, sleep until 7 AM someday!
Good luck with your little one! And let me know if you find a way to get your daughter to sleep through the night!