What do you think Gene means when he states that he "lost part of" himself to Finny and realizes that his purpose had been "to become part of Phineas."

I think both characters are foils for each other until they (almost) merge together. Their attraction to each other seems to transcend friendship, love and even the sexual. These two guys want to become each other or a communion in the most literal sense. I think this relationship went both ways. Both boys were obsessed with each other's very being. Perhaps part of this was latently sexual but there seemed to be a fascination which transcended this.