Here's my noted. I more or less boiled down the run to the actions you take. Not the prettiest display, but maybe it'd be useful for someone else too. Was able to sort most of this out on my own in a blind playthrough. Had help from gamefaqs for a couple sticky spots.
Pick new game [start timer]
MOVE Mt Enriku (Action stage, Sent to Summit after boss)
MOVE Izumo [SPLIT]
LOOK Noodles
TALK Kuma twice
MOVE Izumo Temple
LOOK Black Spot, Light Rectangle
MOVE Outside
TALK (Boss Battle)
TAKE Charm
MOVE Izumo
TALK Kuma Twice (TAKE Noodles to heal)
MOVE Summit Temple
TALK about Kusanagi
MOVE Attaro Shrine [SPLIT]
LOOK Sword
TAKE Sword (Boss Battle)
TALK
TAKE Sword
MOVE Summit Temple
USE Charm
TALK about Iwato
MOVE Mt. Miwa [SPLIT]
USE Fake Sword (Battle)
MOVE Inside, Outside, Summit Temple
TALK
MOVE Kashima Temple [SPLIT]
LOOK Sword Twice
TAKE Sword (Boss Battle)
Take Sword
MOVE Summit Temple
===============Sea section=================
MOVE Shimono-seki [SPLIT]
LOOK Terrain Twice
LOOK Girl
CAST Hatten, Makiri, Kannon
TALK Girl three times
MOVE Midori's House
TAKE Food to heal (optional)
MOVE Pier
LOOK Boat House
TALK
MOVE Boat House
LOOK Terrain
MOVE Outside, Midori's House
TALK
MOVE Pier, Boat House
TAKE X-Ray Glasses
MOVE Outside, Sea [SPLIT]
MOVE Right, Front, Left, Front, Right, Front, Right, Jump in the Ocean
CAST Kannon (move to Lute)
MOVE Left, Back, Back
USE Lute
MOVE Jump in the Ocean (Get Vajira)
MOVE Left, Front, Left, Left
USE Lute
MOVE Jump in the Ocean (Get Helmet)
MOVE Front, Front, Jump in the Ocean (Move over bracers after beating Fish boss)
MOVE Right
USE Lute
MOVE Right
USE Lute
USE Beads
MOVE Jump in the Ocean (Action Scene-go right, swim down holes)
CAST Kannon
LOOK Sword
TAKE Sword
MOVE to Boat
USE Sword after scene (Sent to Summit) [SPLIT]
=============Get Spaceship===============
MOVE Izumo
MOVE Izumo Temple (Boss Fight)
MOVE Inside
MOVE Outside Twice (Boss Fight)
TALK
TAKE Ball of Shimazu
TALK
MOVE Izumo
TALK Kuma
MOVE Kumano Temple
LOOK at Terrain
TALK
USE Ball of Shimazu
TALK
MOVE Kakogen [SPLIT] (Down Well, Makiri avoid falling. Press down on Stone.)
LOOK Round Depression (Might need twice)
CAST Indra
USE Ball of Shimazu
MOVE Inside of Pot
LOOK at the Hand-shaped button
MOVE Outside (Leave area / Energy Grind?)
TALK
MOVE Mt. Hinokami [SPLIT] (Two Bosses)
LOOK Bracer twice
TAKE Armor Bracers
MOVE Kumano
USE Armor Bracers
MOVE Kakogen (Down well again, GRIND ENERGY IF GOING TO. Press down on Stone.)
MOVE Inside of Pot
USE Armor Bracer (Transport to Pyramid) [SPLIT]
===========Pyramid==============
MOVE East Side
CAST Fudo
MOVE Inside
(Go all the way right, Get pyramid, die and/or leave area left)
CAST Makiri
USE Pyramid
CAST Makiri
MOVE East Side, South Side, Inside
(Go up first stairs, beat flying thing for hammer)
(Go Far right door. Enter first door to the right. Enter First door to the Left)
(Cast Makiri(Fly) break topmost blocks to the right, get Leg Armor. Fly all the way left, get Trident)
(Go up stairs to the right, beat eyeball thing. Enter 2nd door on the right)
(Cast Makiri(Fly), break topmost blocks of the pillar to the left for Body Armor. Fly Left enter door left of stairs)
(Kill goat thing, enter 2nd door to the right)
(Enter first door to the right. Climb up stairs to exit).
TALK four times (Then boss fight, sent back to Summit, then to Underworld) [SPLIT]
==========Underworld==================
USE Sword of Kusanagi
TALK
MOVE Misty Crossing, Gate
TALK
MOVE Chizu Sea
TALK
LOOK Nectar Bottle (Can TAKE to heal)
MOVE Misty Crossing
USE Nectar twice
TALK
MOVE Yomotsu
(Enter Tree door) USE Sword of Kusanagi
MOVE Outside
(Up 1st Stairs from entrance) TALK twice
MOVE Outside
(Up 2nd Stairs from entrance) MOVE Outside
(Go left back to Tree) TALK, MOVE Outside
(Go Left to boat) MOVE Toki Plains
LOOK Rock
TAKE Object
MOVE Misty Crossing
TALK
TAKE Oar
MOVE Toki Plains
USE Oar
TAKE Harp of Amano
MOVE Chizu Sea
USE Harp
MOVE Misty Crossing, Yomotsu
(Go right and up 2nd Stairs)USE Harp
MOVE Outside (and return left to boat)
TALK (sent to thunder god fight - move onto sword after winning) [SPLIT]
MOVE Yomotsu (back to 2nd stairs)
USE Sword of Fury, TALK, MOVE Outside (back to Amano's tree)
TALK, MOVE Outside (all the way to the right)
MOVE Right four times.
USE Sword of Fury
MOVE Inside (Medusa fight. Move onto mirror.)
MOVE Right four times, then Outside
(Left to 1st stairs from left) USE Mirror. TALK (Sent to Summit) [SPLIT]
==========Last Stretch============
MOVE Izumo
LOOK Kuma's Necklace twice
TALK Kuma. TAKE Necklace
MOVE Kashima
USE Sword of Branches
USE Mirror
USE Sword of Kusanagi
(Final Boss rush) [SPLIT]
