Brainwashing and a False Persona, Your take on a quandy I am having. Options

[Ezra]

Right, so I am finally getting my hands on being able to play SR again, after a year of GMing. (Plastic Rat is going to be Gming the group for a while.)
The character concept that I want to play is a little complex, but I figure it shoudl be cool to play.

He is an escapee from an MK-Ultra/ Manchurian candidate style military organisation. Basically, he was X, but was brainwashed and "re-programmed" to believe that he is Y. He escaped from the military group wuite by accident, and now is a shadowrunner, quite convinced that he is Y. He has no memory of ever being part of the military group, and is staying in the shadows for other reasons. (that have no bearing on this problem)

He has no memory of the military group, and has no memory of being X. He is however, Y....a fully developed and skilled magic user.

NOw.....I was looking through the edges and flaws and was trying to find a logical starting point for him.

Amnesia doesn't fit. Even at it's lightest (-2), he would have no memory of his past life. Which is true to a point. However, he has a full memory of his life, albeit false.
So Amnesia doesn't really fit.

Dark Secret. Again, this flaw requires him to have knowledge of his secret, so that he can act against it being found out. He has no memory of anything other than him being Y, so he has no real Dark Secret flaw.

Hunted. This one fits to a certain extent. HOwever, he wouldn't know if he had an enemy or not. (Besides, for the sake of a lasting character, I am writing into his history that they believe him dead. No one wants a covert intelligence/spy/military organisation with unlimited resources (Rating 6 enemy IMHO) chasing you from the beginning.

So....I am a little at a loss.
What do you guys suggest? Is this covered anywhere that I should be aware of?
Thanks.