I didn't save the Ship, but I just maxed out shields as fast as possible to avoid Damage, then maxed Weapons.
Sold my Drones and rockets etc. and ended up with I don't know how many Crewman of what Race scattered everywhere, with a triplelaser, basiclaser, some hotgun or something ( a big purle laserbeam I think), and a healing shield Weapon. No extra Slots or anything, on Pomaos Ship v2.