From the palace start, move right and step onto the bright tile. Head through the door it opens to find a few Rupees.
Return to the entry room and shoot the orb across the gap with an arrow. Move across the new platforms and head through the door. Look left to see another orb. Shoot it open the leftmost door in the entry room. Head through that door to grab a Red Rupee from the chest.
Head back through the center door in the entry room. Cross over the bridge in the following room to reach an area with rolling boulders.
Carefully make your way up the boulders' path, then take a left. Head through the door on the left wall. In here, you'll battle a group of Like Likes. This will spawn a chest on a ledge you can't reach from in here. Exit through the lower door.
Head up the stairs and exit through the northern door. You're now on the ledge with the new chest. Open it for the Compass. Drop from the ledge and walk south into it to find you can pass through. Hit the tile in the room you reach to spawn a chest containing a Red Rupee.
Make your way back to the outer part of the same room and step on the tile on the upper right. Head through the door it opens to find yourself on ledges above the rolling boulders. Follow the platforms to cross over the boulder's path. Head north between the Armos to find a tile you can step on. Head through the door it opens.
In this room, there are two orbs: one you can shoot while the platform is low, and one you can shoot when it rises. Hit them both then quickly move into the corner of the room you can now access. There's a Small Key in the chest here. Exit to the left to return to the rolling boulder room.
Head to the locked door at the north end of the room and use your Small Key to reach the second floor. Step on the switch and battle the Armos to open the doors and spawn a shortcut portal.
Take a right from the portal room. Step up to the narrow ledge, then follow it southwest to find a tile you can step on. This opens the way out. Also, note that there are a few Like Likes that appear if you explore the room. Kill them all to spawn a chest containing Monster Guts.
Now take a left from the portal room. Dodge the boulders in here and step on the light tile to slowly extend some stairs. Dash up them before they retract, and follow the bridge down to the other side of the room. Step on the right light tile here to retract the stairs you just descended. Step on the tile they reveal a chest containing Monster Guts. Step on the left light tile to open the way out of here.
Head through the door. In the next room, head up the stairs, then down the second set. Move to the northeast corner of the room. From here you can shoot an orb to the left. Do so to activate a moving platform. Step onto that platform, then fire an arrow at the northern orb when high enough. Head through the door this opens.
Step onto the moving tiles and ready your shield and bow. You need to shoot the four orbs in the middle of the room while darts shoot at you from the walls. Keep your shield handy, and it won't be too tough. Once all four are hit, a chest containing a Small Key appears. Grab it and return to the previous room.
Step up to the center platform and move toward the big locked door. Turn left and shoot the orb to activate a second rising platform. Use it to reach a locked door which can be opened with your Small Key.
In the proceeding room, take out the trio of Stalfos to lower the chest to your level. Open it for the Big Key, then exit through the southwest door. Slash the orb here to lower a block surrounding one last orb near the big door.
Return to the room with the big door and ride the left platform up. Fire an arrow at the last orb when high enough to flip the center platform, giving you access to the big door. Use your Big Key to enter the boss chamber.
Yuga is pretty easy to best in this battle. Fire an arrow over the pit to stun him, then get in a few swipes. Take out any Soldiers he spawns, and keep hounding him. The battle will end quickly.
Return to the dungeon entry room with your new Merge power. Slip through the crack on the right side of the room to find a Silver Rupee in a chest.