If by chance you test positive for anything he will have to be treated also.
Are you sure the pain during sex was associated with the birth control? Have you thought of getting chlamydia and gonorrhea test done? Actually be tested for all std's.
Because vaginal opening has nothing to do with your urethra I am not sure about this burning, it all takes me back to a possible infection of some sort. It could be something simple but to have a infection of any sort for so long can cause fertility issues in the future.
I think your best bet is to speak with a gyn and have a pap smear done as well as any additional testing for infections. There are so many different things that can cause the problems that you have