I have mitral valve prolapse and even though it's so insignificant ( between stage 0 and 1), ive done extensive research on my condition after I was diagnosed and asked lots of questions. From everything that I've read, if you've had any type of valve replacement you need to be on antibiotcs BEFORE the dental procedure and continue taking them after the procedure (for as many days as your dentist prescribes). Have you warned your dentist of your condition? If you have and he hasn't put you on antibiotics I suggest you see a cardiologist and have them prescribe them to you.
Go back to your dentist, it sounds like you do have an infection starting and there should be no pain after a root canal because there is no nerve in the tooth to hurt.