Does this ability work for the ship it is assigned to in addition to all other ships?

In order to use this ability for all ships in a turn do I need to activate the ship it is assigned to first or can I use the card at the start of the ship phase even if I don't activate the ship it is on first?

An engineer command won't trigger the ability it has to be a token or discard?

1. Yes.

2. No you don't. Yes you can.

3. Exactly.

Follow-up question: can the ship only use tokens that belong to it, or can it use another ship's token?

Last question on this and thanks for the quick help

If I'm the second player do I use STM after the first player has completed his first activation?

Negative. It happens at the start of the Ship Phase, which is the phase during which ships are activated. It's the sane timing as Han, so if one player has Han and the other has STM, Player 1 does his first, then Player 2.

Keep in mind, though, that the shields are not all recovered at once, but rather as each successive ship activates.

Indeed. Han, Tarkin, Reinforced Blast Doors and all the fleet command upgrades all trigger at the same time.

Do I have to discard the token from the ship having the upgrade card to activate the card's ability (I'm pretty sure the answer is yes)?

Yes, "you" on an upgrade card refers to the ship to which that card is equipped.