There's a key to making the 2nd and 3rd stages of the boss trivial, and that is to take out all its crew, except for the one crewman manning the lasers during the first wave. The boss won't regenerate crew between battles, BUT if you kill all crew it becomes AI controlled so it can self repair. If you keep the laser guy alive during that first wave if you have any amount of shields you can take your time to whittle away his crew any way your ship is able to manage. Usually a combination of missiles/bombs + boarding parties should be enough to whittle his crew down.
After his crew is dead, the second and third forms become a matter of having either stealth to overcome the drone wave or the giant salvos, or maxed shield+evade. Then pretty much any weapon/boarding combo should be enough to whittle it down.