Like lordfuzun said, Costume Change Tokens are for your character, not your ship. Whenever you commission a ship you get 1 free Rename and 1 free ship customization (not including changes to bridge or layout). Anything else after that, and you have to pay EC to the Ship Tailor.
I haven't been able to requisition a ship with them.
You are not getting a free ship at VA. You can buy it from C-store, with zen. Also, ship you received at level 40 is good for everything.
You can easily buy a ship from exchange. Mirror universe ships are cheap and easy to get.