First things First , do not attempt the perfect boss runs until you have maxxed the Photon Launcher. Also if you get hit by the boss , simply die and continue and try again. The checkpoints are just before each boss in the game
Method for the Boss Fight
Keep Shooting and when the boss gets close jump up , dash up and then dash over the boss. Keep doing this until the boss is at half health.
He will now throw away his shields.Next just back up in to a corner while you keep shooting the boss. Whenever he approaches jump straight up and then dash up. In this time the boss will have changed direction and you can drop straight down safely to resume your assault.