Pretty sure your weapon damage doesn't make any difference. Definitely not enough to be worth worrying about, anyway. (Speed and armor do matter, though.)
Easiest way to take out Keller is to fly around the edge. If you stray into the center, you'll likely collide with the other ships at which point you're toast. Concentrate on avoiding being hit rather than on hitting them.
Best weapons in reverse order: Torpedo (makes it trivial), vertix, flow blaster (fly backwards!), multi-resonator.
Also, if you have the droid junior, use it! It will constantly, slowly, replenish your health.
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