I replaced the housing on my iPhone SE and ran into the same problem — Apple Pay didn’t work. After a lot of troubleshooting, I realized that the NFC antenna contact was misaligned. This is an old post. I’m posting my solution to spare the next person who runs into this from the headache. The offending contact is here: The circled screw secures the NFC antenna (built into the power button flex cable) to the motherboard. Note the small, metal, inverted “J” coming out of the left side of the screw. That exposed piece of metal, pictured here: Needs to make contact with the motherboard pad pictured here: (Ignore the highlights around the two chips. We’re looking at the line on the top left of this photo.) It’s very easy to either place the motherboard on top of the ribbon or to screw the surfaces together sideways, resulting in poor contact between the two components. Good luck!