pms is pretty common in women. that pain probably has to do with how your body responds to the hormones released during those days. stomach problems are also common with or without pain killers.
problems with your bladder is not related to trans or cis as far as i know. both men and women have these problems, and it's mostly to do with your immune system, but infections can also be related to intimate contact with another person. the body is weaker to bacteria it hasn't encountered before. drinking enough, using the toilet regularly, and keeping warm are some ways of preventing those infections. some people are also unlucky and have the wrong genes. hrt might have upset your immune system and made you more susceptible to infections for a while, for all we know, but that's not really trans related. there are more than enough other medication that can mess up your body in unpleasant ways.
some std's can cause similar symptoms. worth checking out if you have been careless once, even if it's been a while.