Gastroesophageal Reflux Disease (GERD): The symptoms of coughing only when lying down, particularly on one side, and difficulty breathing could be indicative of GERD. Lying down can exacerbate reflux, leading to coughing and breathing difficulties due to the irritation of the respiratory tract by stomach acid.

Postnasal Drip: Also known as upper airway secretion syndrome, this condition can cause coughing, especially when lying down, as mucus drips down the back of the throat.
Asthma: Although asthma can cause coughing and difficulty breathing at any time, certain triggers, including lying down or nighttime, can exacerbate symptoms in some individuals.
Chronic Obstructive Pulmonary Disease (COPD): COPD can cause chronic cough and difficulty breathing, which may worsen in certain positions or at night.

Pulmonary Embolism: Although less likely, a pulmonary embolism can cause sudden onset of difficulty breathing and cough, which may worsen when lying down due to increased pressure on the lungs.
Pneumonia: Certain types of pneumonia can cause positional cough and difficulty breathing, and it's crucial to diagnose and treat promptly to avoid complications.
Heart Failure: Congestive heart failure can lead to orthopnea (difficulty breathing while lying down) and paroxysmal nocturnal dyspnea (waking up with shortness of breath), which could be mistaken for a primary respiratory issue.

Bronchiectasis: A condition characterized by damaged airways, leading to chronic cough and difficulty breathing, which might worsen in certain positions.
Cystic Fibrosis: Although more common in younger populations, cystic fibrosis can cause chronic respiratory symptoms, including cough and difficulty breathing, which may have positional components.
Lymphangitic Carcinomatosis: A rare condition where cancer spreads to the lymphatic vessels in the lungs, causing respiratory symptoms, including cough and difficulty breathing, which might be positional.