You must travel to the tops of the clouds in order to open the way to the next element.
Explore Veil Falls
If you go down and into the water below you can reach a piece of heart. There is also stuff to collect if you enter via Lon Lon Ranch. Anyway, go north to a stone door, with which you can fuse your gold Kinstone piece. The door opens, go through.
Turn on your lantern, head right and up the stairs. The fiery skull thing can be defeated with the boomerang. There is a bombable wall between the two blocks in the corner, so bomb it and go through. Inside you get 50 mysterious shells. Continue upstairs and out of there to reach a chest containing 100 mysterious shells. Go back in. You need to push the blocks to the right out of the way and then push the top block left with three Links. Head down, and exit out of the first outside door you saw.
Climb the rock face, and check the tombstone at the top to reveal another Wind Crest. If you did the fusion a chest will be here, containing a blue Kinstone piece. Continue north to enter a cave. Bomb the wall to the east to get to a chest containing 50 mysterious shells. The stairs down take you to a room with a bunch of rupees, plus pools of water that have rupees if you dive down. Outside, you can get in the water but there's nothing you can do there now, so just go back to the room you started in. If you take the right hand stairs you reach a chest containing 100 rupees. Go outside and climb up the wall.
You'll see something moving here, and will hear Goron noises. If you played Ocarina of Time you'll know what this means. For now, just ignore it and head for the big whirlwind at the top of the falls. Jump in and you get rocketed into the sky.
Fuse Kinstones with the two people here. You can talk to them for more info. To continue, walk into the red whirlwind to get projected higher. Continue to the right to reach a chest containing a gold Kinstone piece. Be sure to dig through ALL of the clouds, some hide Kinstone pieces. Then fall into the hole by the chest to get to a different area of the clouds below. Go north to another red whirlwind and take it. Go north again and you'll have to break out the mole mitts to dig through the thick clouds. Drop down the hole above. Fuse your gold Kinstone with the mysterious cloud and one of the pinwheels by the entrance will start spinning. You need to get all of them spinning to get out of this area. Take the red whirlwind back up.
You will need to hop into the white whirlwind to float in the air. Float left and a little down to another whirlwind, and continue left and a little up to another cloud to land on. Drop into the hole here. You need to kill the two cloud piranhas to get your next gold Kinstone piece. Let them charge at you and stay still, it'll jump over you and you won't get hit. As it's falling back toward the cloud, hit it. They need to be hit twice to be beat. Once done, then fluffy cloud above will break apart, revealing a gold Kinstone piece. A red whirlwind also appears, take it back up.
Dig west through the thick clouds to reach a regular whirlwind below. Jump in and head left and up (not southwest) to another cloud surface. Dig away the thick clouds to find a total of 100 mysterious shells up above, and a gold Kinstone piece below. Go back to the regular whirlwind and take it straight south. You may have to use the whirlwind slightly to the right to keep going so you can get around the thick clouds and land on the surface. Drop down the hole here.
To kill the Lakitu you can use the boomerang to stun it so you can hit it, or shoot it with arrows, up to you. Go north to fuse Kinstones with the cloud. Go back down below and use the red whirlwind.
Above, use the regular whirlwinds to float slightly right and down, then left and down to the lower-left cloud. Dig out the chest containing 50 mysterious shells. Fall down the hole.
Go north, kill the Lakitu as before, and go up to fuse another gold Kinstone. Use the red whirlwind right here to reach another gold Kinstone piece. Fall back down below, continue south to the lower area, and use the rightmost red whirlwind.
Fall down the hole. Kill two more cloud piranhas for another gold Kinstone piece. Use the red whirlwind where the Kinstone piece appeared, and grab the 50 mysterious shells from the chest. Use the regular whirlwind and head southeast to another cloud surface. Dig through the thick clouds to discover a small hole, and jump in. Use the nearby red whirlwind, then fall down the next hole. Fuse your gold Kinstone with the mysterious cloud. One more fusion left. Take the red whirlwind back up.
Get into the regular whirlwind and head left to the next cloud surface. Dig through the thick clouds to reach another regular whirlwind. Go a little up then right, hit the next whirlwind on the way, then start heading south until you reach the cloud surface and a hole. Drop down it to reach the entrance of Cloud Tops. Fuse your last gold Kinstone with the mysterious cloud below. The last pinwheel will spin and make the fluffy cloud break apart, revealing a large whirlwind. Take it on up.
House in the Clouds
First things first, check the tombstone to create a wind crest up here for much easier access. Then go on up into the house (Ezlo will ask the obvious question: how'd they build a house up here?)
There may be Kinstones to fuse with the people here if you didn't do it before. If you go up through the regular doorway (not the stairs) you reach a room with that warp tile in it... this is the same building you warped to from South Hyrule Field! Go on upstairs, and make sure to visit Gregal, who, if you sucked the ghost away earlier, will give you the Light Arrows! Head upstairs once again. In the room above, there are three chests, the left two containing blue Kinstone pieces, the right containing a red one. Go up the stairs where the woman is standing, and in the room above are two chests, each containing a red Kinstone piece. First fuse Kinstones, TWICE, with the person here (I think someone on the first floor said the person is an old woman). Then talk to her and she will grant you access to the Palace of Winds. Talk to the kid blocking the stairs, and the way to the fourth floor will be opened. Go up, break the pots (a couple hold fairies), use the giant whirlwind, and you reach the Palace of Winds.