Your flying hours will count towards FAA licences but your JAR theory exams will not. They won't count for nothing since the knowledge you gained studying for them will help with your FAA exam study although you'll have to learn many rules, regs & procedures afresh.
As I recall you'll also have to do a minimum of 3 hours with an FAA instructor to be recommended for the flight test. You'll also have to ensure that you meet the FAR min. experience requirements for the FAA licence.