Hi, and thanks for your medical question on eHealth forum!
Pain in the clitoris could be caused by injury as you suspect due to over masturbation. It could also be due to vulval or vaginal infection. Another possibility is a peripheral artery disease or a peripheral neuropathy.
It is difficult to diagnose the cause on net. Hence, it is not possible to advice treatment. If it is injury and it is a nerve injury, then chances of healing are less. If it is infection, then the type of infection will have to be identified like bacterial vaginosis or a STD or a non specific inflammation. Blood should be tested for diabetes and hypothyroidism. It can also be pinched nerves and the nerves can get pinched at the spine or in pudendal canal (pudendal neuralgia).
Since a confirmed diagnosis cannot be given on net please discuss these possibilities with your gynecologist once. Hope this helps. Take care!