It is a good sign that your actual urine is clear ! This means that your kidneys work fine and there is rather mechanical problem/cut/bleeding area.

It does sound like a relatively comon problem called 'Jogger's hematuria'. Google it. It is a case when an empty bladder's walls can rub up against each other and cause capillaries to break. Many marathoners have the condition after races. Also, bicyclists can get it because of "impacts" to "that" area.

However, it is very crucial that you get that check out immediately. If you go to ER, do not be modest about your symptoms. Slight overstatement will get you treated faster!

Good luck!

EDIT: Just read your reply - good luck with the kidney stones! I am very sorry but it is one of the better diagnosis ...