I made a glitch compilation from my TAS testing a while ago, the quality isn't great, but it gets the point across.
http://www.youtube.com/watch?v=IMhFCZvfkPk
If you get a superswim going, you can swim near land to refill air without losing speed and go back to speeding up. This is how the final video clip occurs.
The early route is something like this. It is very rough, and may have blatant errors.
1: Jump off watchtower.
2: Superswim glitch into Forest of Fairies to trigger cutscene so game doesn't crash later.
2: Grab 100 rupee chest under grandma's house (This takes about 55 seconds, there may be a more optimal way to get 80 rupees through manipulation.)
3: Superswim to Windfall (buy sail (80) (The sail is needed before FF1, or you get caught in a text lock. The text lock may be avoidable with perfect input that I wasn't able to do.) (Let Tingle Out (1))
4: Superswim to Greatfish to trigger endless night (required to get bombs)
5: Superswim to Northern Fairy Isle (Get Rupee Upgrade 1000)
6: Enter nearby sub, Lantern Moblin + No Sword sends you to Forsaken Fortress 1
7: Trigger Tetra text at bottom of FF1 by stairs. Beat Forsaken Fortress 1 (FF1) (You get a sword here)
8: At Windfall, Get Bombs (Let Tingle Out (2))
9: Superswim to Dragon Roost, get wind waker, get wind requiem
10: Superswim to Bomb Island, get bottle
11: Superswim to Forest Haven, get FOREST WATER (20 min), zombie hover deku leaf
12: DRC deku leaf entry, deku leaf bomb drop the pot, get grapple, clear dungeon
13: Superswim to Bird's Peak Rock, grapple glitch to get triforce chart
14: Rupee collection etc, is forest water BK skip good?
15: FOREST WATER Boss Key skip (20 min later) In my testing, doing 11-15 with no rupees took about 14 minutes of game time, decently optimized.
16: Place pearls, Jabun,
get Rupee upgrade in Forest of Fairies assuming game crash has been mitigated.
17: Tower of the Gods (big skip at beginning)
18: Forsaken Fortress 2 (FF2) (Helmrock superswim, zombie hover past boss fight to loading zone. (You get a shield now if i recall, but still have starting clothes, lol)
There is a softlock with the master sword if you don't go through the first instance of Hyrule, which is triggered by Tower of the Gods. I think this means that Tower of the Gods must be done before FF2
It may be faster to just just the forest water boss key skip and do the dungeon normally. It's hard to work forest water into the run because you have pick it up exactly 20 minutes before you want to use it.
Certain places like Forest Haven, you can't re-air while superswimming, so do a short superswim to a nearby island (e.g. Bomb Island) and then without stopping, get air and start speeding up again.
Also, old but good:
http://www.youtube.com/watch?v=51Xr2JBWbUo
EDIT: This testing was all done in summer of 2011. I captured the videos yesterday from savestates I backed up.
EDIT2: Random Discussion
You need a sail to open triforce charts. You have to open triforce charts for that triforce piece to be acquirable. The position is assigned upon opening the chart.
The crash in forest of fairies is
likely because it tries to load two cutscenes at once; tetra is hanging from the tree and two guys are trying to lift the rock you have to bomb. I'm convinced the only traditional way around this is to watch a certain cutscene early on in the forest. I'm not sure if you have to get tetra down from the tree or not. (Correction:) due to not watching many early game cutscenes. You can kill the enemies in there by having them damage each other or have them take fall damage.
The sail softlock: After FF1 I think, the boat engages you in repeated conversation telling you to get a sail. Supposedly if you sidehop or roll or something instantaneously, you can get away. I was never able to accomplish this, hence I got the sail first (This loses maybe a minute at most.) This needs more testing.