Regards! 1. The conditions are absolutely unrelated. 2. Please look for the stream of urine, if it’s single stream, baby not crying during passage of urine, no ballooning in the prepuce area, then sit back and relax. Any manipulation of the prepuce May further lead to injury. 3. The swellings likely cause seems to be epididymitis if hernia has been ruled out. A non infected epididymis swelling generally resolves in its own course, though if infected might need antibiotics. Judgement on that May require examination and further few testing.

More information is needed e.g. exact location, type of cyst, it's content like pus, water, chylous etc. Kindly take proper consultation. As per penis opening, I think you are telling probaly about phimosis. If yes, it may require intervention.