So is there a doctor or nurse here that answers questions? I haven't had much help with anything on this site :(
The dark spots can be cherry angiomas or benign skin growths also but if he is having painful lymph nodes then it needs evaluation. Lymphadenopathy (swollen lymph nodes) is usually caused by a viral or bacterial infection along with other numerous causes. Treatment is usually cold compresses,over the counter anti-inflammatory analgesics(pain killers) like acetaminophen or ibuprofen,antibiotics if cause of infection is suspected to be a bacteria and surgical drainage if there is any abscess formation.
You should get the spots evaluated and preferably a biopsy done to confirm the diagnosis.
It is very difficult to precisely confirm a diagnosis without examination and investigations and the answer is based on the medical information provided. For exact diagnosis, you are requested to consult your doctor. I sincerely hope that helps. Take care and please do keep me posted on how you are doing.