Good questions, probably no easy answers as I am a leader also.
BSA has removed the restriction on gay scouts, however I think they would view a trans-girl differently.
That said, I would nail down the Eagle, through Court of Honor (Just to make sure)
Not sure of any scholarships directly tied to Eagle rank, most of those are from outside organizations, many of whom I would suspect frown upon transition.
Venture Crew, being part of BSA, would have the same openess to gay scouts, however ranks in Venture do differ from traditional Scouting and there is no Eagle rank.
Could you continue, that would be a question for higher-ups, like National. You may be allowed to stay in Venture as it is co-ed, but no guarantee. However, as it stands right now, leaders may not be trans.
A couple years ago I received a survey from National and suggested that opening up leadership to trans-people would be desirable, I can't say I have heard any further discussion at that level.
Congratulations on Star and best wishes on your way to Eagle.
And basically, I've been holding back on transitioning until my son gets his Eagle - he's life now.