Hookshot to the grate and go through the Boss door behind it.  Watch the short story sequence and you'll have to fight a third Iron Knuckle.  This one is bigger though.  First Z-target him and get fairly close.  Then wait for him to start to swing his axe.  Immediately push Back+A to do a backflip, then push A again as soon as you land to do a Jump Slash and nail him when his defense is down.  Then just wait for him to come close and start another swing and do it again.  Once he's gone, watch another story sequence then go through the door behind the throne.  Go down the hall, through the door, and climb up onto the big square platform.  Step in the middle of the platform to initiate the battle with...

Spirit Temple Boss:  Twinrova

First, jump onto one of the 4 side platforms and face toward the big platform in the middle.  Keep facing toward the general direction of the witches.  Do NOT Z-target.  When one of them looks like she's about to fire, face her and hold down your shield button.  Her beam will reflect off of the shield.  Try to direct it at the other witch by moving the shield.  If they fly over and start hovering above your platform, jump to the middle platform and reflect the attack, then jump back onto your platform.  After you've gotten them to hit each other enough times, they'll combine into a more powerful (but much less ugly) Twinrova.  Jump back to the main platform.  Z-target her and hold down your shield button.  Your shield will absorb her attacks!  After three of the same type (fire or ice) it will fire back at her.  She'll fall down to a platform.  Let off your Z targeting, get over to her platform (Hover Boots may be useful here) and let her have it with the sword.  Then get back to the main platform and repeat the process.  NOTE:  If she fires an attack of the opposite kind of what your shield is absorbing (an ice attack when you previously absorbed a fire attack) just dodge, don't try to absorb it, otherwise you'll get hurt enough to lose 10 hearts!!  Watch the somewhat funny death scene, grab the heart container, and step into the blue light.