I've done the Forest Temple and Phantom Ganon 2nd phase takes 3 cycles to kill him, 2x Master Sword Jump Attacks per cycle. The loss on this version isn't as bad as King Dodongo because the Phantom becomes vulnerable to attacks much sooner.
You can beat him in 2 cycles. Keep close to him, hit fireball back at him at Jump Slash range, jump slash immediately to hit him as he falls, but before he touches ground. If you did that right, you bounce back a bit. Mash out two more Jump Attacks, and they will land (you'll be perfectly aligned so you won't slide left/right/behind him after jump attack animation). Just did this on boss rush mode.