Hi. Thanks for the reply. I wanted to use the ability to change the modules on the ship so that I can use the parts used by crystals on the samatra attack.
Your ship will be extremely powerful even without those slots.
My advice? equip your FlagShip with 50 crew, one high-effective fuelsystem, one A.T.S. (AutoTrackingSystem), two Shiva furnaces and one Hellbore cannon in the second slot. Why the second slot? To shoot a double shot, double damage for the same amount of energy usage. And they clean up most fighters and blades on their way to the target too.
For me that was always more than sufficient to eliminate all guards (Kzer-Za and Kohr-Ah), in most cases without any crew losses. Just make sure you have sufficient distance to the guards when shooting in their direction, to allow the A.T.S. to curve your shots sufficiently to hit. Your engine should be more than strong enough for that. With the Kohr-Ah shoot, take a short break and shoot again. Otherwise your further shots only fall victim to the Fiery Ring of Inevitable and Eternal Destruction (F.R.I.E.D.).
That was also the reason why in the original PC game I only used Avatars vs. the Sa-Matra, as I never had ship losses until I got there. The BumpingTool took it all once the Chmmr equipped it. By now I know I should've left some spare room, to reap the benefits of having started a civil war. Only UQM teached me the joys of having Furies on board with the showdown.