The United Methodist Church has significant number of parishes which affirm LGBT Christians without making a comprehensive policy. It is well known when an ordained pastor came out and transitioned and remained in ministry as Drew Phoenix. Even before that, The UM Church has had no official policy on transgender topics.
In 2002, the Methodists' Baltimore-Washington Conference was home to a similar dispute, when the Rev. Richard A. Zomastny had a sex change and became Rebecca Ann Steen. Steen withdrew her reapplication for ministry under pressure from fellow Methodists. (Source)
In 2008 at the Methodist general conference, some ministers attempted to create legislation that would prohibit transgender people from ordination and remove Rev Pheonix's ordination retro-actively. The movement failed in before coming to the general assembly. The debate of homosexuality and church structure took priority, leaving too little time for consideration of trans issues.
http://www.bwcumc.org/content/statement-rev-drew-phoenix Personal statement