When it says you can take or assign focus tokens to your ship, does it have to be the ship Rey is assigned to? Is this one of those deals when "you/your" means the Pilot, not the player?

Come on, just think about it. Did "you" ever signify anything besides "you" when there's no mention of "other" ships?

"You" means the ship, not the player, in about 99.999% of cases. In fact, it's explicitly defined that way in the rules.

"You" means the ship, not the player, in about 99.999% of cases. In fact, it's explicitly defined that way in the rules.

Not 99.9%, 100%.