Does Kagis' ability interfere with the FCS upgrade? If, for example, a B-Wing with the FCS fires at a Bomber and Kagi is within range 3 of the B-Wing can Kagis' ability force the TL onto his shuttle?

No, FCS specifically states you may target lock the defender, so that is not really an option. Otherwise if you were able to lock on to anyone Kagi would come into play.

Just my humble opinion

There has been some time ago an extensive debate about this very same topic that you may find interesting.

http://community.fantasyflightgames.com/index.php?/topic/89625-fire-control-system-vs-captain-kagi/

Cool, thx.

Sorry, should have pointed you there. There is some debate

Kagi specifically states "When an enemy ship acquires a target lock, it must lock onto your ship if able".

Fire-Control System specifically states "..., you may acquire a target lock on the defender".

My thinking is thusly: Fire-Control says you are able to acquire a target lock on one ship (the defender). As you are unable to target lock Kagi unless he is the defender, you cannot target lock Kagi as per his own rules.

Now, if you were running a Shuttle (Sssay, Col. Jendon) with a Fire-Control System and a Weapons Engineer, the target lock you're able to acquire from the Fire-Control System triggers the Weapons Engineer, giving you one target lock on the defender and one on Kagi.