Finding and resurrecting the Eagle
From the entrance of the Face Shrine you'll want to play the Manbo Mambo song on your Ocarina and warp over to Ukuku Prairie then take a walk to the left into Mabe Village, now make your way into the Trendy Game Shop to the south and win yourself the CiaoCiao Figure. Exit the game shop and make your way into Madame MeowMeow's house to display it on her table.
Head out of the house and make your way to the right to find an Eagle Statue, push it forward to reveal some stairs then go down , go to the back of the area to find an Eagles Skull where you'll need to play the Frog’s Song of Soul near it to resurrect the Eagle. Go back to the surface and make your way over to the Kamlet Castle's gate then take a left, use the Eagle that's following you to hover past the holes and proceed down the stairs, open the Chest to get a Secret Seashell and leave.
Make your way over to the Seashell Mansion and update your Seashell count, upon reaching the fourth milestone you'll be rewarded with the Koholint Sword.
Locating the Bird Key
Use the ocarina to warp on over to Manbo's Pond then head left and up into Tal Tal Heights, continue forward until you approach a sign and remove the stone on the right to find another Secret Seashell. Now remove the stones on the left to free the path up, then follow it along until you reach the second ladder, climb up and listen to what the Owl has to say then enter the cave on the left.
Once your inside you'll want to make your way through to the right and head down the stairs, use the Eagle to cross the gap and open the Chest to find 50 Rupees. Exit the cave out of the door on the right and follow the path of water until you find a waterfall, dive into the water to the right of the ladder to find a Secret Seashell at the bottom.
Climb up the ladder and follow the path around to find a cave entrance, walk in and continue into the next room, here you'll need to position the stones to allow you to use the Eagle's assitance and fly to the room above. Continue holding the Eagle to cross the large gap in the next room to the left where you'll find the Bird Key.
Find the Eagle's Tower
Exit the cave and head up the stairs, use the Eagle and fly across the bridge to the left, remove the plant to reveal some stairs and head down. Use a Bomb and blow up the crumbling wall below and head through, take out the enemies and proceed into the room on the right where you'll find a Piece of Heart.
Make you way back out into the main section of the cave and head left and down the stairs, continue following the path along and fly over the gap to the exit. Follow the path to the left and climb up the ladder, continue following the path and drop down into a rocky area, go left again and collect a Piece of Heart before dropping down.
Note: There is no need to open the Chests in the room as they only have enemies inside them.
Go back up the ladder where the Owl spoke to your recently and use the cave to get to the other side again, head into another cave to the right of the waterfall and place a Bomb against the crumbling wall, proceed through the now open path and take the stairs up. Walk down and position the stones to free your way to the bottom entrance where you'll find a Chest with a Secret Seashell inside.
Head back through the cave and go right from the broken wall and exit, climb up the ladder and follow the path around to the exit, now re-enter the cave through the door on the left and walk down the stairs, hop across the gap and follow the path to the exit below.
Make your way through another sneaky cave entrance to the right and continue up the stairs ahead, then quickly exit through the bottom path and insert the Key into the Eagle's Tower.