How to treat genital canker sores? Hi there, I saw my ob on tuesday. A few weeks ago I had thought I had a UTI but it got better. Well...On sunday the pain came back and I had a canker sore by my urethra. I have never experienced anything like this before

Not canker sores. You need to see your ob/gyn or a dermatologist for these lesion. Two prevalent diseases that give genital sores are herpes(a virus) and lichen planis(auto-immune possibly). Both can be painful and can have oral and skin related lesions. Some cases can become serious from scarring. Talk to your md.
I . I am sorry you are having so much pain. As you are pregnant please contact your OB again immediately and let him/her know how much pain you are in, and see if the cultures are back. You may need prescription medicine to treat your infection and your pain. Your OB will want to know that you are having worsening symptoms.