IIRC Fire-Linked means that if you fire mulitple weapons at one target then you use a single to hit roll for all those weapons.  You can still split your weapons between targets.

I find shields 0 works fine, especially if you then add a house rule that says that non-piercing applies to them so the weaker weapons have a small chance of not damaging a regular ship (i.e. if you use non-piercing -1 against Shield 0, then you need to roll 2 or better to damage).  You end up with fairly bloody and quick engagements.  I was trying to make races that use some shields, like the Abbai and some Brakiri, stand out from other races that just use a thick hull to protect themselves.

I think ships such as the Shadows and Vorlons with high shield values should be seriously scary in this setting.  IIRC the first Shadow ship they took down with firepower during the series (rather than an exploding jump gate) was hit by lasers from a number of ships - these were either heavy lasers (Imp 2) from the Narn cruiser or neutron lasers (Imp 2) from the Sharlin or similar weapons.  I think that shows that you either need to use weapons with a Impact better than 1 or a serious amount of other weapons, preferably both, to deal with the Ancients - probably right for the setting.