Clicking sound from engine

My fiance has a GZ250 and its made a constant clicking sound while running for 3-4 months now. It was low on oil about 3-4 months ago, so I wonder if that's the cause of the issue. If so, any idea on what might have been damaged, and what possibilities there are to fix it? I do all the maintenance on my ninja, but am certainly not a professional mechanic and have never done intense engine work.