I too am having this issue on my iPhone 6 Plus running 8.1.2, but this was caused not by a system restore, but simply by logging out of iCloud and logging in again. (I did this to remedy an issue with my calendars not syncing). Had I known that this would also remove my stored Apple Pay cards I probably would have tried another solution.
After logging back into my iCloud account (and also rebooting for good measure) I was unable to add any of my credit cards back to Apple Pay and would get the error "Could Not Add Card: Try again later or contact your card issuer for more information."
I just spoke to Bank of America's Apple Pay support team and they're stumped, since all my BofA cards are working fine and ready-to-go for Apple Pay (at least on their end). However, they informed me that they aren't able to really do anything unless the card is already added to Passbook, and pending authorization. This allows them to see it on their own system, but since iOS is preventing me from even adding the card, their hands are tied.
I even tried adding my Chase card and I still get the same error.
I really don't know what to do at this point, and I really don't want to have to go to the Apple store just to have them swap my iPhone out for a refurbished model.