… kid that finally died by getting shot at the end I think..anyway the end is EPIC-the town people do the autopsy on the young man and take off the clothes to realize this tough boy was actually a girl the whole time. May have taken place place in a wooded area, probably somewhere between Montana and Colorado the 60’s or 70’s. And I think the she male character had befriended a wolf that they just shot on her last stand! I saw the movie in the late 90’s as a kid.
Could it be Boys Don’t Cry? http://en.wikipedia.org/wiki/Boys_Don%27t_Cry_%28film%29
I think you might be remembering “The Ballad of Little Jo.” your description fits pretty well.
http://www.imdb.com/title/tt0106350/?ref_=fn_al_tt_1