I have the same problem. I have a pain at the tip of my penis and some cramping pain in my back sides and abdomen. The most troubling is the pain at the tip of my penis. My urologist told me I have blood in my urine and he scoped me into my bladder and said all looked clear. I am next having a CT with resolutionon my kidneys. I have been uncmfortable or a month and I am sure I have some stone or syst. Until i read your post, I didnt know the relation to kidney stones of your penis.
If you're not seeing a Urologist (sp??), here are some natural methods of helping:
http://www.earthclinic.com/CURES/kidney_stones.html
http://www.areclinic.org/articles.asp?ArticleID=7&src=m
I'm 68yo and have never had a kidney stone, but I have been drinking a mixture of ACV & water for about 15-20yrs... is it the remedy?? I have no proof, but possibly so !?!?