Short (3 min) episode of rapid thumping heartbeat slowed back to normal when taking a deep breath. could this be serious?

Palpitations: It sounds like you didn't have symptoms of chest pain, dizziness or shortness of breath. Then most likely it isn't serious but if this has not been evaluated by your physician you should do so. Minimize caffeine or any other stimulants such as smoking or decongestants. If there is a family history of heart disease of any kind then take this seriously.