Here's an old(ish) manga that fits the bill:
http://mangafox.me/manga/mahou_shounen_majorian/
Only 4 chapters have been scanlated, but I know for sure that the manga was completed and RAWS were available online at one time. It is about two boys who transform into magical girls. The story has far more depth to it than just that and the RAWS seemed to suggest that it would have been an interesting read. It also features some interesting transformation sequences:
