I know I’m a little late to the party, but I have to throw in my two cents for anybody that is still having this problem. In short, I rebuilt my iPhone. Everything worked flawlessly. That is, except for Apple Pay. I realized this once I went to a restaurant and attempted to use Apple Pay to purchase the food, but to no avail.
So I then reopened the phone and realized that the problem laid within my re-placement of the NFC bracket interconnect, and that it was not seated correctly to ensure an electrical connection. I didn’t take any pictures to describe what I’m talking about. There’re pictures of what I’m talking about in the iFixit guide listed above, but to describe in words; the upper part of the interconnect bracket must be seated under the camera bracket, instead of over it. If placed over it (like I had it), then the plastic part of the camera bracket will act as a insulator, therefore stopping the near field communication signal from consistent successful transmission. The metal (copper) part of the interconnect needs to be touching the metal part of the housing, and screwed down tightly but not overly tight, to ensure a secure electrical connection to the antenna of the iPhone.
I hope this helps somebody out there!