Modified from bakenekos route http://pastebin.com/tKnsRLi9
Main route change is fire arrows before water temple and water cs skip
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MST Route for N64 v1.0 (Improved Ama's MST Route Idea)
s = Deku Sticks, n = Deku Nuts, c = Bombchus, b = bombs
-Beginning-
・Collect 35 rupees
(You may get Kokiri Swrod but in that case you don't have to equip it until collect BotW Chus)
(I don't know if getting the Sword is faster but at least it makes child section easier)
・Buy 2 Deku Sticks and Deku Nuts (s2,n5)
・Correct 7 rupees and go to Lost Woods
(you need 50 rupees for buying a fairy before DMT
7 rupees at Kokiri Forest + at 16-18 rupees at Zora River + 25 rupees at Spirit Trial = 48-50 rupees
if you couldn't get enough rupees, you have to get extra rupees somewhere)
・Naviless Aquaescape
・WESS to Kakariko (s1)
・Collect Cuccos for Bottle (n4)
・Navi Dive to BotW
-BotW-
・Blank A for Bombchu (n3,c10)
・Vine Clip with Chu, get Hylian Shield and Deku Shield (or get a small key for 2 shields) (c9)
・Death or Savewarp
・Go out and savewarp
-Jabu-
・Go to Lost Woods and Aquaescape
・Over the fall with megasidehop (c8)
・Get a fish
・Get Stick and Nuts from pots (s2, n8)
・KZ Skip (c7)
・Enter Jabu (s1/optional)
・Switch (c6)
・Hiking with Ruto
・Beat Stingers with Stick ISG and get Boomerang (n7)
・Box Mega (c5)
・Beat Barinade with Stick ISG (n5)
・HC, Savewarp
-Deku-
・Get on the top of the House of Twins and hover to Deku Tree CS Skip (c3)
(For the safer route, hess past mido to save a chu, and use the chu to hess to kak at beginning of adult)
・Kill Deku Baba for Stick (inside deku if you skip the cutscene, on the way to deku if you don't)
・B1 Skip with jumpslash or Baba megasidehop (be careful about the amount of sticks)
・231, Gohma (n4)
・HC, Ganondoor, Savewarp (n3)
-Trial Chus, Zelda and DoT Skip-
・Collect Silver Rupees in Spirit Trial (n2/optional)
(If you have only 1 stick, be careful not to break stick when Beamos hover)
・Stun Slugs and jumplash the switch for Bombchu chest (n1, s0, c23)
・DO NOT Bombchu the switch
(Don't forget to make sure you have 1/4 or half a heart)
・Go out and enter to the crawlspace
・Zelda and Lullaby CS Skip (don't save & continue) (c22)
・Go to Temple of Time and Swordless DoT Skip
-Opening of Adult and Shadow-
・Savewarp
・Hess to Kak if you did not skip deku cs earlier
・Go to Graveyard
・Dampe race for Hookshot
・Chu-slide Teleport and enter to Shadow (c21)
・Dead Hand and get Hover Boots
・Boat Skip and BK Skip (c17)
・Bongo (dupe a bottle over Nuts slot if you can)
・CS Skip
-Bolero and Magic-
・Go to Potion Shop and buy a fairy (don't forget bottle duplication)
・DMT HESS to Goron City (c16)
・Megasidehop Clip to Darunia room (c15)
・Deathless Bolero CS Skip
・Go to Great Fairy Fountain and get Magic (c14)
・Megaflip to DC (c13)
-DC-
・Blow up the wall (c12)
・Savewarp for WW
・Doom Jump
・Get the Bomb Bag (b20)
・Megaflip into head (b19)
・Hoverslide to Boss room (b17)
・Blow up the floor (b16)
・Get bombs from chest (b20)
・KD (b18)
・WW to GTG (b17)
-Spirit-
・Go out and be caught by guards
・50r in box on top of jail
・Gate Skip
・Across Wasteland (HESS if you can) (b16)
・Across Desert Colossus (SS if you can) (b14)
・Spirit Hover (need to be very fast) (b12-13, c3)
・Hoverslide to Mirror Shield chest (b10-11)
・Iron Knuckle
・Get a small key and pray to Bomb God (b20)
・Go up to the top floor
・BK Skip (b17)
・Nabooru Knuckle and CS Skip (b16)
・Twinrova
・CS Skip (b15)
・Play Bolero
-Fire-
・Enter to Fire
・Darunia CS Skip and get the 1st small key
・Get 2 small keys (b14)
・Block Skip and get a small key (b13)
・Continue through Fire...
・Flame wall maze Superslide or HESS and over the last wall with damage invincible (b11-12)
・Blow up the wall and get bombs from pots (b20)
・Flare Dancer
・Switch (b19)
・Hammer
・BK Skip with Hess (b18)
・Volvagia (b11)
・WW to Forest
-Forest-
・Get the 1st small key
・Beat Stalfos and get the 2nd small key
・SoT Skip with Ledge Clip
・Megajump to the upper floor (b10)
・2 Block Skip with Groundjump (b8)
・Continue through Forest...
・Beat Stalfos and get Bow
・BK Skip with Hammer Recoil
・Phantom Ganon
・CS Skip (b7)
・Play Bolero
-Water-
・Enter to Goron City
・Hammer + hover boots clip to goron shop, but 10 bombs (b17)
・Go to Lost Woods (break the rock with hammer)
・Aquaescape
・Over the fall with Hover Boots
・Ladder Clip and go to Lake Hylia
・Hess to back of the water temple island and climb from behind, kill GS on top of the tree with chu (c2) (b16) (very tight on night time here)
・Shoot sun
・GS hookshot jump to fire arrows
・Megaflip ground clip to water temple OoB (b15)
・Enter to Water
・Across gap with Hoverslide (SS, HESS, Megasidehop, Hammer Recoil or TEKTITE) (b14)
・BK Skip (b11, c0)
・Morpha
・CS Skip (b10)
・Savewarp
-Trials-
・LACS
・Go to Ganon's Castle
・Weirdshot in Spirit Trial (b9)
・Clip into Light Trial and finish (b7)
・Fire Trial Collect silver rupees (Golden Gauntlets Skip and collect the last one with Slug or a bomb) and fall then open the door
・Across the gap with Megasidehop Hoverslide or Hess and finish Fire Trial (b6)
・Shadow, water, forest trial normally
-Tower and Collapse-
・Dinolfos, Stalfos, Iron Knuckle
・Hess up stairs (b5)
・Ganondorf
・Collapse Skip (b4)
・Double Kiss if you have enough bombs (b2)
・Ganon (b0)
・Complete!