The setup is players in a freighter versus Imperial NPCs on an Imperial Customs Frigate, there will be shooting in space.

This is pretty straightforward Sil 4 VS Sil 4 space combat; except that I don't have stat blocks for my appropriately-trained Imperial crew.

What published NPCs should I use for the dice checks I'll need for the badguys?

Captain (for Leadership checks): Customs Inspector (EotE 397)

Pilot (for Pilot checks): ?

Engineer (for Mechanics checks): ?

Comms Officer (for Computer checks): ?

Gunners x6: Imperial Gunnery Corps (AoR 418)

It looks like you have AoR which has all of the basic crew for Imperial ships. Check out AoR 419-420. There are a couple of generic enough Imperial minions that you can tap into and modify as needed.

Oh, the Incom Engineer, that might work!

Captain (for Leadership checks): Customs Inspector (EotE 397)

Pilot (for Pilot checks): Imperial Pilot (BtR:78)

Engineer (for Mechanics checks): Incom Engineer (AoR 413)

Comms Officer (for Computer checks): Incom Engineer (AoR 413)

Gunners x6: Imperial Gunnery Corps (AoR 418)

If they are part of the ship, and not intended to be met "in person", you could just assign a stat to each roll as you would a character, and not worry about name of opponent or any stats. i.e.

Customs Corvette:

Leadership: YYGG

Pilot: YGG

Mechanics: YY

Gunnery (minion): GGG (guns can be grouped as desired)

Cool: YYG

etc.

I use Oggdude's GM tools, it's set up to allow assigning NPCs to crew slots. This is a fun feature.

There is a modular encounter in Suns of Fortune that covers this well.