1: You won't need a new set of prints. Even if they tried to charge your card and it was declined, they're supposed to contact you about it.
2: I don't have personal experience with this yet, but the CIC won't request your FBI background check until they start to work on the applicant's portion of the application, which usually happens at least (normally more than) two months after SA, depending on the VO. Just make sure you write a letter explaining why you haven't sent the FBI PCC up front. If they do request the FBI PCC and give you a set number of days to send it and you don't have it yet, write another letter explaining the same thing. It's if you don't try to contact them about it where you can have some issues.
Personally, I was unable to open the packet to look at my prints. The lady who took my prints taped and signed the envelope and said my prints would be invalid if the packet was opened before the FBI reaches it. Any fingerprinting technician is aware of how to take legible prints like these, it's just sometimes people have very very poor fingerprints.