Can over-masturbation cause permanent harm to a penis? I masturbate nearly every day and sometimes for long periods and my penis has ached for weeks.

Slow down tex. I think you are answering your own question. If you are masturbating enough to make your penis hurt I would back off on frequency / intensity / duration until that is not the case. Masturbation is a healthy thing but the penis itself is still a soft organ and you can hurt it. Unlikely to do permanent damage but still.