Hello, and thanks for your medical question on E Health Forum.
From the history provided it seems that your pain might be more of a musculo-skeletal origin that any systemic disorder.
Proper exercise routine and relaxation after workouts, and good nutrition might solve all of your current issues.
In case of mild pain or aches, OTC tylenol or ibuprofen might relieve your symptoms.
Presence of respiratory problems like cough, dyspnea on exertion might be associated with exercise induced asthma, which might need to be evaluated with pulmonary function tests and a Xray, and then treated with appropriate inhalers or oral medications.
I hope this helps.