What Causes Muscle Soreness?

yes i have a question, I had a bump on the shaft of my penis i went to my doctor and he said that i had lesion of syspilis but then he test my for it i did not have it and he gave me a oral exam for herpes and i did not have it, but i had a urinary track infection,i was treated for that but im have musle soreness in my upper back,my calf,shoulders and my knee and my penis has a little skin peeling under the head,i went back to my doctor and he said im clean i dont have any infection,i havent worked out i about a month and a half could that be why i have musle soreness?