If my ship has FCS and targets a ship with Rebel Captive (immediately get a stress), can FCS trigger after the attack?
FCS does not state that this is an action, but the wording "Acquire a target lock" is the actual wording for that action.
So is this a free action, that you can't take if stressed, or assumed to be just the acquring of tokens?
Acquire is entirely different from a free action. You can "acquire" any token if you're stressed or not; you cannot do a "free action" if you are stressed.
So yes, FCS works even after you fire on a target with Rebel Captive.
Think of it this way, the Target Lock Action lets you "aquire a target lock", just as a focus action allows you to "assign a focus token". However, the actual aquire and assign is not the action its what you do as a result of performing the action, and other things (such as FCS) let you aquire and assign without performing the actual action.
Think of it this way, the Target Lock Action lets you "aquire a target lock", just as a focus action allows you to "assign a focus token". However, the actual aquire and assign is not the action its what you do as a result of performing the action, and other things (such as FCS) let you aquire and assign without performing the actual action.
That's such a confusing way to put it, I had to read it twice to find out what you were trying to say...
Think of it this way, the Target Lock Action lets you "aquire a target lock", just as a focus action allows you to "assign a focus token". However, the actual aquire and assign is not the action its what you do as a result of performing the action, and other things (such as FCS) let you aquire and assign without performing the actual action.
That's such a confusing way to put it, I had to read it twice to find out what you were trying to say...
oh, good, it wasn't just me then? 
If my ship has FCS and targets a ship with Rebel Captive (immediately get a stress), can FCS trigger after the attack?
FCS does not state that this is an action, but the wording "Acquire a target lock" is the actual wording for that action.
So is this a free action, that you can't take if stressed, or assumed to be just the acquring of tokens?
Things are only actions if they say that they are actions; if they don't say that they are actions, you are permitted to do them when you are stressed unless they specify otherwise.