How do I reconcile my gender views with my Judaism?

I think your issues only pertain to more conservative/extreme facets. In the reform movement, circumcision has been increasingly less common since the 1980's. I myself am an uncircumcised reform jew born in the 80's. As for the gender issues, unfortunately when you look at the extreme ends of any culture or faith, you will find some problems. If you stay more on the liberal or centrist end of things, these issues are practically nonexistent.