I got to the boss and had cloak, which protected me from missiles while i used the bio beam to kill crew members in the gun rooms. then i used a 5 laser burst to break through shield and hit twice.
It worked well, albeit slow. I had almost everything maxed out.
However, his 3rd part absolutely ruined me. His super shield took too long to break through with only 1 5 burst laser. i could only get 1 hit off maybe before you puts up the super shield again.
This game is one of those games where you experience and learn from your mistakes. ITs still luck based, but you can get skilled enough to bypass the unlucky moments.