@thedrake Hi Mark, Thanks for getting the Pirate supplement, it is a fun add-on to the main rules, and I hope you enjoy the scenarios as well.
Well as I mention in all my supplements and scenarios you could probably use your own rules system with a little work, and that is true with Full Thrust, the main thing is the ships and they transfer over fairly easily, main work is with the weapons…
So for Pirates I would suggest the Anti-ship Torpedo packs are replaced with Submunition Packs, PDS is basically an Area Defence AF system that can destroy missiles as well.
Shields in Stars & Lasers are similar to Defensive Screens, also Missiles and Hardpoints are on the same lines as Pulse torpedoes.
Ship class and hull size should basically be transferable although the Full Thrust ships have slightly more damage points, but this shouldn't matter.
I would keep most of the Pirates weapons as "B" Beams except maybe the biggest ships they could probably have an "A" or two.
And the Pirate Clipper could be something like a Courier Class ship with a "C" Beam.
I would try and keep weapon numbers similar to the Pirates in Stars & Lasers, remember these are not meant to be big military ships.
I hope that helps.
Mac