Control Cucco:
When you find a Cucco, hit it eight times to go into its view and to be able to move it around. The easiest way to do this is just after you get the Iron Boots. Walk outside the building to find a Cucco. Wear the boots and roll into it eight times.
Defeating Twilight monsters:
The easiest way to defeat them is to kill the one that is not near you, then use the force field to kill the rest.
Zelda: Ocarina Of Time reference
The three spirits that watch over Hyrule are a reference to the goddesses in Zelda: Ocarina Of Time. Their names are similar.
Temple Boss - Diababa:
Part I
The boss battle begins with two plant tentacles attacking you - stand near the back wall to avoid their attack. On both sides of them are spider-bombs. Lock onto one of them with your boomerang, then lock onto one of the tentacles and throw your weapon. It will pick up the bomb and then go straight to the tentacle destroying it in the process. Do this again this for the 2nd one as well.
Part II
After both tentacles are destroyed, the boss's real form will be shown. Throw your boomerang towards him to start a little cut-scene. It turns out the baboon that you beat a short while back wants to help you He will swing back and forth carrying a bomb between his feet. Use your boomerang to lock onto the baboon first, then the main part of the boss, and let it go. Like with the tentacles, it takes the bomb towards the boss where it will then explode. After, the boss's head will fall down to the ground - slash it with your sword at the eye when the eye's sticking out. When he runs away, he will fire a poisonous liquid at you. Stand back against the back wall to dodge it. After, repeat the above process to beat him. You will then be awarded with a Fused Shadow and a full Heart Container.