I did a TAS to understand how to get the quick kill. Now that I know what's up, it shouldn't be too hard to do. Here's what I found:

• Equip the first missile.
• position yourself at about one-third of a screen width away from the left edge of the screen.
• fire the missile right when the boss clicky sound stops.
• Right after firing, position yourself directly in the center of the screen, where a new missile would be picked up. Press B and A simultaneously as soon as you have moved to the middle of the screen. If you aren't pretty close to the exact middle, you won't pick up the missile.

A few notes: The first effective frame for collecting the second missile was immediately after firing the first one, frame 18108 in my TAS. The last effective frame was one frame after the first frame that the boss flashed from damage, frame 18203. That is a leisurely 95 frames, well over one second. I had been trying to press B and A at the moment the first missile hit, which made life really hard. I hope that helps.

Now, if I can figure out how to beat the cube boss more effectively. That one's kicking my trash.