Have you tried removing the card from Apple Pay and then adding it again? That will change the device card number used. Also, is BofA showing a declined transaction at all? I know they said that they didn't decline anything, but it would still show if you attempted it.
Yes I have removed and re-added. Still doesn't work. Went through the whole activation process with BoA and nothing.
Also, they see that they have been declined but say it's not them.