Okay, I have a ship with FCS and Weapons Engineer.

The ship fires at a target, blah blah blah, and gets a Target Lock on the defender from the FCS. He can only acquire a TL on the defender as stated in the FCS card. Then WE kicks in. It says "when you acquire a TL, you may lock on to 2 different ships." So now I can TL two ships, and I understand I can TL the defender plus another ship.

However, can I TL 2 **different** ships which does not include the defender? Say I had enemies A, B, C, and D, all within TL range. I target Ship A... can I then use the WE's ability to TL Ship B and C instead and leave Ship A without a TL? Or if I kill Ship A, can I use WE to TL Ship B and C?

This is in the FAQ, under Fire Control System:

No. Since the first target lock is coming from FCS, it must go on the defender. The second lock can go wherever you'd like it to.

As a side note, if you end up killing the defender, then you get neither target lock, because the target is gone by the time FCS kicks in. This stops you getting that first lock and triggering the Engineer.

As a side note, if you end up killing the defender, then you get neither target lock, because the target is gone by the time FCS kicks in. This stops you getting that first lock and triggering the Engineer.

What if you're the same pilot skill? Tied PS allows for simultaneous fire so if you have initiative and roll enough damage to destroy his ship, it's still on the board until it resolves its attack. Shouldn't FCS then allow the target lock to go through? I'm extending logic from the Fel's Wrath/Corran Horn example on pg 11 of the FAQ for this conclusion.

It sure would. And it could be usefull if you allso had say R7 onboard.