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I wrote a small FAQ that hopefully is useful for 100% route planning. Its goal is to concisely outline when what item/event is available.

I played through the game again when making this, but I made an initial draft using http://www.gamefaqs.com/wii/960633-the-legend-of-zelda-skyward-sword/faqs/63413. Descriptions of locations are often partly copied/plagiarized from this FAQ. This is just meant to be a useful document for speedrunners. Suggestions are always welcome.

*** Shows important items/events. These are required to move on in the game.
() Shows locations. The goal of these is just to distinguish what item is being talked about, not to lead you to it if you have no idea where it is.
[] Shows either the cost of an item or the contents of a treasure.
{} Are some additional notes.
The rest should speak for itself.
-----------------------------

*** Practice Sword

*** Sailcloth

*** Goddess Sword

*** Placing the Emerald Tablet

*** Adventure Pouch
- Wooden Shield (Bazaar)  [50 Rupees]
-- Banded Shield (Bazaar) [30 Rupees, 2 Amber Relic]
--- Braced Shield (Bazaar) [50 Rupees, 3 Amber Relic, 2 Monster Claw, 2 Tumbleweed], 1 Ornament Skull]
- Heart Potion (Bazaar) [20 Rupees]
-- Heart Potion+ (Bazaar) [20 Rupees, 3 Blessed Butterfly, Volcanic Ladybug, Woodland Rhino Beetle]
--- Heart Potion++ (Bazaar) [30 Rupees, 3 Blessed Butterfly, 3 Deku Hornet, Eldin Roller, Sand Cicada]
- Revitalizing Potion (Bazaar) [30 Rupees]
-- Revitalizing Potion+ (Bazaar) [20 Rupees, 3 Deku Hornet, 2 Skyloft Mantis, 2 Woodland Rhino Beetle]
--- Revitalizing Potion++ (Bazaar) [30 Rupees, Gerudo Dragonfly, 3 Lanayru Ant, Sand Cicada, 2 Woodland Rhino Beetle]
- Guardian Potion (Bazaar) [200 Rupees]
-- Guardian Potion+ (Bazaar) [40 Rupees, 3 Blessed Butterfly, 2 Eldin Roller, Faron Grasshopper, 3 Starry Firefly]
- Empty Bottle #01 (Bazaar)
- Item check girl conversation #01 {Every subsequent new conversation can be recognized by Link having to select a response.}
-- Item check girl conversation #02 {You need to sleep or clear a dungeon(?) after conversation #01 to trigger conversation #02.}
- Heart Piece #01 (Pumpkin Landing, on chandelier)
-- Task #01 for Lumpy Pumpkin owner, soup delivery
- Empty Bottle #02 (Sealed Temple)
- Heart Piece #02 (Southwest of the Great Tree)

*** Slingshot
- Scattershot (Bazaar) [50 Rupees, 2 Amber Relic, 2 Dusk Relic, 3 Jelly Blob]
- Small Seed Satchel (Bazaar) [100 Rupees]
-- Medium Seed Satchel (Bazaar) [50 Rupees, 4 Amber Relic, 3 Monster Claw, 3 Ornamental Skull]
--- Large Seed Satchel (Bazaar) [100 Rupees, 5 Amber Relic, Blue Bird Feather, Golden Skull, 3 Monster Claw]
- Extra Wallet #01 (Beetle's Airshop) [100 Rupees]
-- Extra Wallet #02 (Beetle's Airshop) [100 Rupees]
--- Extra Wallet #03 (Beetle's Airshop) [100 Rupees]
- Adventure Pouch Slot #01 (Beetle's Airshop) [300 Rupees]
-- Adventure Pouch Slot #02 (Beetle's Airshop) [600 Rupees]
--- Adventure Pouch Slot #03 (Beetle's Airshop) [1200 Rupees]
- Life Medal (Beetle's Airshop) [800 Rupees]
- Bug Net (Beetle's Airshop) [50 Rupees]
-- Bug Medal (Beetle's Airshop) [1000 Rupees]
-- Big Bug Net (Bazaar) [100 Rupees, 2 Ancient Flower, Evil Crystal, 3 Tumbleweed]
- Goddess Cube #01 (Deep Woods, next to Gorko)
-- Goddess Treasure #01 (Pumpkin Landing, next to the building) [Adventure Pouch Slot #04]
- Goddess Cube #02 (Deep Woods, next to gap south of Skyview Temple)
-- Goddess Treasure #02 (Island south of Skyloft) [Heart Piece #03]

*** Beetle
- Heart piece #04 (Skyview Temple, use the beetle to hit the switch at the top in the big round room.)
- Heart Container #01 (After defeating Ghirahim #01.)
- Goddess Cube #03 (Skyview Temple, behind the altar)
-- Goddess Treasure #03 (Pumpkin Landing, above the entrance) [300 Rupees]

*** Obtaining the Ruby Tablet
- Iron Shield (Bazaar) [100 Rupees]
-- Reinforced Shield (Bazaar) [50 Rupees, 2 Eldin Ore, 2 Monster Claw, 2 Ornamental Skull]
--- Fortified Shield (Bazaar) [100 Rupees, Blue Bird Feather, 3 Eldin Ore, 3 Monster Claw, 3 Tumbleweed]

*** Placing the Ruby Tablet
- Talk to Batreaux {This is required to make gratitude crystals spawn and do the gratitude crystal sidequest}
- 5 gratitude crystals (Talk to Kukiel's mom after Kukiel returned.) (5)
- Empty Bottle #03 (Talk to Orielle who is stuck on an island, then to here brother Parrow who will give you a bottle containing mushroom spores.)
-- 5 gratitude crystals (Deliver the mushroom spores to Orielle) (10)
--- 5 gratitude crystals (Talk to Parrow again after delivering the mushroom spores.) (15)
- 1 gratitude crystal (In Links room.) (16) {These stray gratitude crystals can only be collected at night, and unless specified, can be found in Skyloft}
- 1 gratitude crystal (Near the top exit of the Knight Academy.) (17)
- 1 gratitude crystal (Under the ceiling in the Sparring Hall.) (18)
- 1 gratitude crystal (On the small platform slightly to the north of the Bazaar that is can be reached by a small wooden bridge.) (19)
- 1 gratitude crystal (Climb down the vines near the western windmill.) (20)
- 1 gratitude crystal (Inside Orielle and Parrow's house.) (21)
- 1 gratitude crystal (Behind the lone tree next to the big pumpkin field.) (22)
- 1 gratitude crystal (On the Light Tower.) (23)
- 1 gratitude crystal (At the exit of the waterfall cave.) (24)
- 1 gratitude crystal (Where Link's Loftwing was imprisoned.) (25)
- 1 gratitude crystal (Pumpking Landing, on the second floor.) (26)
- 1 gratitude crystal (Pumpking Landing, outside, at the pumpkin storage.) (27)
- 1 gratitude crystal (On Beedle´s Island.) (28)
- Item check girl conversation #03 {You need to sleep or clear a dungeon(?) after conversation #02 to trigger conversation #03.}
-- Item check girl conversation #04 {You need to sleep or clear a dungeon(?) after conversation #03 to trigger conversation #04. Link will be called "Darling" during conversation #04.}
--- 5 gratitude cystals (After conversation #04, Talk to the Item Check girls father (If this is the first time you talk to him, sleep and talk to him again.). Then talk during the day to Item Check girl, who will invite you to her place at night as she has something to tell you. Talk to her at night, sleep again and then talk with her father.) (33)
- Medium Wallet (Talk to Batreaux with 5 or more gratitude crystals.)
- Heart Piece #05 (Talk to Batreaux with 10 or more gratitude crystals.)
- Big Wallet (Talk to Batreaux with 30 or more gratitude crystals.)
- Cursed Medal (Appears in Batreaux's house after talking to him with 30 or more gratitude crystals.)
- Heart Piece #06 (Buy it in Beedle's shop after buying the Life Medal) [1600 Rupees].
- Goddess Cube #04 (Just over an edge close to where you first land when going down to Eldin Vulcano for the first time.)
-- Goddess Treasure #04 (On an Island to the northwest of Beedle's Island.) [100 Rupees]
- Goddess Cube #05 (Take left path at intersection after the second save statue in Eldin Vulcano.)-- Goddess Treasure #05 (Near Fun Fun Island) [Small Seed Satchel]
- Heart Piece #07 (Climb the ledge instead of going over the first skeleton bridge and walk around to reach the ledge with the Heart Piece.)
- Goddess Cube #06 (Descent into Digging Mitts cave, on a ledge.)

*** Digging Mitts
- Goddess Cube #07 (West of the Earth Temple entrance, bomb a wall.)
-- Goddess Treasure #07 (Bamboo Island) [300 Rupees]
- Goddess Cube #08 Cube (East of Earth Temple entrance, alongside the magma river.)
--Goddess Treasure #08(Near Beedle's Island) [Treasure Medal]
- Goddess Cube #09 (Eldin Volcano, during the slide after the high-temperature room.)

*** Bomb Bag
- Heart Piece #08 (Faron Woods, bomb a wall south of the Great Tree.)
- Small Bomb Bag (Bazaar) [150 Rupees]
-- Medium Bomb Bag (Bazaar) [50 Rupees, Lizard Tail, 3 Ornamental Skull, Blue Bird Feather]
--- Large Bomb Bag (Bazaar) [100 Rupees, 2 Hornet Larvae, 3 Lizard Tail, 4 Jelly Blob, Golden Skull]
- Heart Container #02 (After defeating Scaldera.)

*** Obtaining the Amber Tablet
- Task #02 for Lumpy Pumpkin owner, carrying pumpkins.

*** Placing the Amber Tablet
- Goddess Cube #10 (Lanayru Mine, behind the starting platform.)
-- Goddess Treasure #10 (Near Beedle's Island [100 Rupees]
- Goddess Cube #11 (Lanayru Desert, normally you would need the Clawshots to gain access to this cube, which stands on the wall west to the cages where you get the Hooked Beetle, but a forward jump slash in Hero Mode also reaches it.)
-- Goddess Treasure #11 (On an island to the northwest of Fun Fun Island.) [Life Medal]

*** Hooked Beetle
- Quick Beetle (Bazaar) [50 Rupees, 2 Ancient Flower, Golden Skull, 2 Hornet Larvae]
-- Tough Beetle (Bazaar) [50 Rupees, 3 Ancient Flower, 4 Amber Relic, Blue Bird Feather, Goddess Plume]
- Goddess Cube #12 (Lanayru Desert, on a ledge surrounded by sinksand.)
-- Goddess Treasure #12 (Vulcano-like Island to the south of Skyloft [Heart Medal]
- Goddess Cube #13 (On the timeshift stone track near the Temple of Time)
-- Goddess Treasure #13 (Beedle's Island) [Heart Piece #09]

*** Gust Bellows
- 5 Gratitude Crystals (Cleaning Pipit's House) (38)
- Heart Container (After defeating Moldarach)

*** Harp
- Stamina Potion (Bazaar) [50 Rupees]
-- Stamina Potion+ (Bazaar) [20 Rupees, Faron Grasshopper, 2 Gerudo Dragonfly, 2 Sky Stag Beetle, 3 Volcanic Ladybug]
- Give Fledge Stamina Potion #01 (At night, in his room.)

*** Ballad of the Goddess song
- Task #03 for Lumpy Pumpkin owner, playing the harp [Heart Piece #10]

*** Defeat the Imprisoned #01
- Sacred Shield (Bazaar) [500 Rupees]
-- Divine Shield (Bazaar) [100 Rupees, 2 Bird Feather, Dusk Relic, 3 Ornamental Skull]
--- Goddess Shield (Bazaar) [150 Rupees, 3 Bird Feather, Blue Bird Feather, 4 Dusk Relic, 3 Monster Horn
- 5 gratitude crystals (Get Carlin's letter, for which examining the Restroom door at night may be needed. Give it to Karane or to the ghost in the Restroom. (43)
- 300 Rupees (Talk to Batreaux with 40 or more gratitude crystals.)
- 5 gratitude cystrals (Retrieve the Party wheel) {After retrieving the Propellor.} (48)
-- Heart Piece #11 (Win 500 Rupees on the Fun Fun Island)
- Goddess Treasure #06 (On the Isle of Songs) [300 Rupees]

*** Farore's Courage song

*** Water Dragon's Scale
- Air Potion (Bazaar) [20 Rupees]
-- Air Potion+ (Bazaar) [20 Rupees, 2 Lanayru Ant, 2 Sky Stag Beetle, 2 Skyloft Mantis]
- Goddess Treasure #09 (Skyloft, Swim through the hole below Kukiel's house.) [Heart Piece #12]
- Goddess Cube #14 (Faron Woods, Drop down to the cube right after exiting the Great Tree for the first time)
-- Goddess Treasure (Skyloft, Skydive to the small Island) [100 Rupees]
- Goddess Cube #15 (Faron Woods, drop down at the first cubby hole after the bird statue on the Big Tree. This can also be reached with Clawshots from the ground.)
- Goddess Cube #16 (Faron Woods, drop down from the Big Tree near the spot where you are attacked by bats.)
-- Goddess Treasure #16 (On an Island to the northeast of the Isle of Songs.) [Rupee Medal]
- Goddess Cube #17 (Laka Floria, near the orange bird statue in the tunnels.)

*** Whip
- Heart Container #04 (After defeating Koloktos)

*** Farore's Flame
- Give Fledge Stamina Potion #02 (At night, in his room.) {gratitude points cannot be obtained until after Nayru's Flame.}

*** Nayru's Wisdom song

*** Clawshots
- Goddess Cube #18 ((Lanayru Desert, roll a bomb over the fake quicksand, and use the clawshots to reach the ledge.'
-- Goddess Treasure #18 (Northwest of Bamboo Island) [Heart Medal]
- Goddess Cube #19 (Lanayru Sand Sea, Jump on boxes in the harbour and Clawshot across.)
-- Goddess Treasure (Bazaar) [300 Rupees]
- Goddess Cube #20 (Skipper's Retreat, Clawshot to
 vines to reach the platform.)
-- Goddess Treasure #20 (Northwest of Fun Fun Island.) [Potion Medal]
- Goddess Cube #21 (Pirate Stronghold, (after clearing stronghold building Clawshot onto ledges.)
-- Goddess Treasure #21 (Skyloft, at the top of the waterfall.) [Heart Piece #13]
- Goddess Cube #22 (Deep Woods, use the Clawshots to reach the vines at the east side outside of Skyview Temple),
-- Goddess Treasure #22 (Beedle's Island) [Rupee Medal]
- Goddess Cube #23 (Lake Floria, use the Clawshots to reach the high ledge.)
-- Goddess Treasure #23 (Below Fun Fun Island) [300 Rupees]
- Heart Piece #14 (In Zelda's room.)
- 1 gratitude crystal (In Zelda's room.) (49)
- 1 gratitude crystal (At the top of the waterfall.) (50)
- 5 gratitude crystals (Find and deliver the missing baby rattle) (55)
- Giant Wallet (Talk to Batreaux with 50 or more gratitude crystals.)
- Goddess Treasure #14 (Volcano-shaped island south of Skyloft) [Heart Piece #15]
- Goddess Treasure #15 (volcano-like island to the south of Skyloft) [Heart Piece #16]
- Goddess Treasure #17 (Skyloft, a small island that can be reached by jumping from a ledge at the top of the waterfall.) [300 Rupees]

*** Bow
- Heart Piece #17 (Sandship, climb the mast and use the Clawshots to reach the chest.)
- Small Quiver (Bazaar) [150 Rupees]
-- Medium Quiver (Bazaar) [50 Rupees, 5 Amber Relic, 3 Dusk Relic, 3 Monster Horn]
--- Large Quiver (Bazaar) [100 Rupees, 3 Dusk Relic, Goddess Plume, Golden Skull, 2 Monster Horn]
- Iron Bow (Bazaar) [50 Rupees, 2 Eldin Ore, Evil Crystal, 3 Monster Claw, 3 Tumbleweed]
-- Sacred Bow (Bazaar) [100 Rupees, 2 Evil Crystal, Goddess Plume, 3 Lizard Tail, 5 Tumbleweed]
- Heart Container #05 (After defeating Tentalus.)

*** Nayru's Flame
- Heart Piece #18 (Shipyard, Rickety Coaster mini-game faster than 1:05)
- 5 gratitude crystals (Talk to Fledge during the day after giving him Stamina Potion twice) (60)
-- Heart Piece #19 (Play the Pumpkin Pull mini-game and score higher than 600 points)

*** Din's Power song

***Fireshield  Earrings
- Goddess Cube #24 (Volcano Summit, skydive off the ledge at the spring.)
-- Goddess Treasure #24 (Bug Rock) [Heart Piece #20]
- Goddess Cube #25 (Outside of Fire Sanctuary entrance, climb through the window on the east side.)
-- Goddess Treasure #25 (Isle of Songs.) [Small Bomb Bag]

*** Mogma Mitts
- Empty Bottle #04 (Fire Sanctuary, defeat the a Lava hand.)
- Heart Piece #21 (Fire Sanctuary, catch the Mogna.)
- Heart Piece #22 (Just outside the Fire Sanctuary, burrow into the hole in front of the Gossip Stone.)
- Heart Container #06 (After Ghirahim #02.)

*** Din's Flame
- 5 gratitude crystals (Find a plower for the Lumpy Pumpkin girl.) (65) {Lumpy Pumpkin tasks must be completed.}
- Heart Piece #23 (Talk to Gorko and draw the correct symbol on the wall.)

*** Defeat the Imprisoned #02

*** Talk to Zelda in the past
- 5 gratitude crystals (Retrieve the fortune teller's ball.) (70)

*** Spiral Charge

*** Bilocyte
- 5 gratitude crystals (Talk to Beedle at night and retrieve his Horned Colossus Beetle by beating the bug collecting game in 3 minutes or less.) (75)
 {You will also get a 50% discount on your next purchase at Beedle Airshop.}
- Talk to Owlan to aquire dowsing for a rare plant.

{The order of obtaining the dragons' songs does not matter.}

*** Defeat the Imprisoned #03
- 5 gratitude crystals (Deliver a Kikwi to Owlan.) (80)
- Tycoon Wallet (Talk to Batreaux with 80 gratitude crystals.)
*** Water Dragon's Song

- Goddess Cube #26 (Volcano Summit ride the moving platform on the lava river.)
-- Goddess Treasure #26 (North of Bug Rock.) [Empty Bottle #05]
*** Fire Dragon's Song

- Goddess Cube #27 (Lanayru Gorge, near the Life Tree Seedling)
-- Goddess Treasure #27 (North of Bug Rock) [Small Quiver]
*** Thunder Dragon's Song
- Heart Piece #24 (Play the Thunder Dragon's Boss challenges until he offers it.)
- Hylian Shield (Play the Thunder Dragon's Boss challenges until he offers it.)

*** Song of the Hero

*** Stone of Trials

*** Triforce

Pretty godly so far. I'll use part of this for my any% planning if that's okay. As a reference

Also, I don't think potions need to be included. Maybe not even shield upgrades

This seems good. The upgrades will be a tricky part if you haven't gotten treasures in a former adventure. It seems you planned to get items before the neccesary ingredients are aviable somehow.

Yeah, I assume(d) that such a run will be done in Hero Mode.