Well then, I'd say you at least got your money's worth!
But seriously, this is why I don't trust Japan's healthcare system, hospitals or doctors for jack shit. It is a flawed, ass-backwards system and the only upside is it's socialized and cheap. This is the same healthcare system that royally fucked my stomach up for four years until I finally left and went back to a real doctor stateside. I came in with acute peptic ulcer symptoms and was 1) refused a barium scan, 2) refused an endoscope, and every one of the next six or seven times I came back with even worse symptoms I got the same treatment--doctor touched my stomach, grunted about possible gastritis or perhaps minor ulcer, stuck me on an IV for an hour because I was supposedly dehydrated and then sent me home with the Japanese equivalent of Tums antacid tablets. It took a year and me having to finally scream at them to get H. Pylori antibiotics and acid blockers and by then it was far too late. I ended up using stupid shit hippy homeopathic remedies until I could get on a plane to go back home and go to a real hospital again for scans, xrays and proper treatment. When I told my doctors here about the "care" I received in Japan they didn't even believe me.
There are a good six or seven possible reasons why your balls may be aching, blue balls aside, and while I'm no doctor it certainly doesn't sound like a vein issue (varicocele) to me. Sorry I'm not able to recommend anyone, but I would seriously look for a non-Japanese doctor or clinic and get another opinion. Perhaps a Korean or European doctor? That's what I did for my dentist, rather than continue going to the "recommended" Japanese clinic with equipment I hadn't seen since the early 1980s. I found an American-educated Korean dentist who didn't accept NHS and charged 10 times more but did dental work from this century. Even my dentist today stateside laughs his ass off at the metal filings I received in Osaka, always asking when I'm ready to pull those fucking things out and get real fillings. As he says: "The second a patient opens his mouth I can tell if he's from Japan because I haven't seen that sort of shitty metals used in over thirty years."
When it comes to your genitals, I wouldn't fuck around and trust Japanese medicine. Go get a foreign opinion, if possible. There must be somewhere in Tokyo with competent, non-Japanese people. It might cost more but it'll be worth it.