The following strategy could save ~40 Seconds. Via shooting at the wall while still in the room, and bouncing the Energy Balls into the holes, you can get the extra Three Energy Balls prior to the Hunter Fights, while completing the puzzle. These are the approximate positions you'll need to shoot at:

• First Shot, shoot at the Red Dot
• Second Shot, shoot slightly above the sign.
• Third Shot, shoot in a position where the Quick Save message is slightly above the sign. As for the Hunter Fights:
• In the First Fight, you'll need a High Pitch Death Sound, or the battle will Softlock.
• In the Second Fight, you cannot kill him prior to him touching the floor, or the battle will also Softlock.

And for the third energy ball, could u kill the final boss with it?

As I remember, no. And on the final boss there are boxes of energy balls for ar2, aren't they?

Yes, there's a Box of Energy Balls during the Finale, and the Final Boss doesn't instantly die to them.