Have you tried messing with the Player/PlayerFemale NPC's properties?
I did notice that one, but being an editor novice I wasn't sure if that was really the player character sheet or not...some of the other stats/description in it sounded a bit off. But I suppose I'll try it anyway.
You should make a custom race (right click in the list and create a copy of the race you will modify -don't forget to make it playable if need be) before editing it unless you want every character in the game to look like they're giants. That's the best way if you don't want to use the console.
I'm not trying to make all the 'generic Khans' change height or something, only the companions & myself. Named npc's have separate stat sheets where you seem to be able to define height/weight just for them. For instance, by default (I didn't change anything) they made Arcade Gannon noticably taller than most others, for some reason, including taller than your character. Changing CraigBoone height hasn't affected anyone else that I've noticed. *knock on wood* heh
But I'd like it more if my female Courier was shorter rather than others being taller. I'm very short in real life and sometimes I want a game to reflect that I have to look up at people all the time. It amuses me.