Re: I really don't know whats happened to me.
Ok, first, congratulations on making positive healthy choices for yourself. That is great news.
Second- PLEASE go see a doctor. Blood in your urine can be serious. Your symptoms are not something you should be seeking help from us here but rather a doctor.
As to the cause- it's possible that you did some sort of internal damage by running but I really doubt it. I think it's more likely this is something else, perhaps an infection. Please, see a doctor, and keep up the positive lifestyle.