In english we talk about aches, pains and niggles.
In german I have never found a good translation and although there are a few forum topics on the subject I stiff havent found a good german alternative.
Pain = Schmerzen - a general term for all kinds of pain whether physical or mental. For me generally quite strong pain.
Ache = similar to a lingering, dull pain of maybe less intensity but longer lasting. Soreness and ache could be interchangable to a certain extent. Ache does not have to be unserious. I have been suffering from hip ache for years due to arthritis. Very uncomfortable and quite serious as it could lead to a hip replacement. But nevertheless an ache. I would almost always say that most most "Enzündungen" result in an ache!
Niggles = the sort of pain or ache that short lived and comes and goes. I think a niggle reflects the view of the person who is suffering and his/her refusal to go to the doctor and get it treated.