Big credit to Fqceless for almost routing late 1-3 and helping me edit the guide. :)

Have tab over 'Menu'. Hold your mouse approximately here so you can enter run training as soon as possible.
https://imgur.com/bcCJ3Fy
Start mashing space and left click to close the menu and enter + start running training.

Running 1 (500 points per level):
Go as far as you can in your first cycle, then if your first cycle is:
<18k - Go as far as you can a second time. (If you don't get enough to reach level 44 on your second cycle, check this again to see what to do for your third, fourth, etc.)
18-22k - Get as many levels as you need to reach level 44.
>22k - Exit running training.

When you die in training:
If you intend to go back into the minigame (i.e. you got <18k), buffer space inputs by holding it down. This will restart the minigame as soon as possible. Be careful not to press any keys after you start holding down space or it will not buffer the inputs. Also note there is about a 0.5 second window between holding down space and when it will start buffering inputs.

If you intend to leave the minigame, hold your mouse in the bottom right so you can click the menu button then immediately start eating seed. Eat 4 seed.
https://imgur.com/Zp3e6cp

Click 'Enter Race' (position your mouse over the button while your duck is eating the last seed).
Tab Space x2 to enter 1-1.
Once the race ends, press Tab Space. If you do this too early, you'll exit the race before it finishes so make sure to wait until after the screen transition.
Click 'Enter Race' (again try to have your mouse pre-positioned during the race).
Click 'Amateur Races' .
Tab Space to enter 2-1.

[I will only cover buying Skill Seed once - henceforth 'SS']
Enter the shop (pre-position).
Tab Down Down Down then hold space to buy Skill Seed.
'Menu' (pre-position while buying SS).
Tab Left Left then press space rhythmically to eat Skill Seed. As a general rule, try to have a new Skill Seed reach the duck after he finishes the eating animation for the previous one.

While your duck is eating the last Skill Seed, have the mouse over 'Train Swimming'. As soon as you see the last yellow bar appear (sublevel), mash click and space to enter + start swimming training as quickly as possible.

Swimming 1 (500 points per level):
Aim for 40k to reach level 89 or 90. Either is fine, but try not to be outside that range. If you get a seed glitch with 88 swim (maybe even without seed glitch) you can lose 3-3 and if you go above 90 you're going to lose time from having to get extra flying levels (you'll probably reach 146 swimming too early). If you don't make it just keep going for more cycles until you do. Remember that if you know you're going to die you can buffer space inputs.

'Menu'.
'Enter Race'.
Tab Space.
1-3.
'Enter Race' (pre-position).
Click 'Amateur Races'.
2-3.
SS.
'Train Running' (pre-position).

Running 2 (500 points per level).
You're aiming for a level between 110 and 115, with a higher level giving you better chances of winning 3-1. 3-3 shouldn't be an issue if you got 89-90 swim.
110 - ???
111 - Basically suicide.
112 - Unlikely win.
113 - Likely win.
114 - Very likely win.
115 - (Probably) certain win.

'Menu'.
'Enter Race'.
Click 'Expert Races'
3-1. A good split (end of race) is sub 7. Sub 6:30 is crazy good.
SS.
'Enter Race' (pre-position).
Click 'Expert Races'.
3-3.
SS.
'Enter Race' (pre-position).
Click 'Amateur Races'.
2-2.
SS.
'Train Flying' (pre-position).

~~Flying 1 (5000 points per level):
Your first few cycles to get you to level 60 will depend on your flying level (which in turn depends on how much Skill Seed you've eaten):
45 - 25k 20k 30k
46 - 20k 20k 30k
47 - 15k 20k 30k
48 - 20k 20k 20k
49 - 15k 20k 20k
50 - 20k 30k
51 - 20k 25k
52 - 20k 20k
Always adjust depending on sub levels. For example, if you're on 48+2 bars, only get 18k on your first cycle (2k less than if you were on 0 bars).
From lvl 60 to 130, alternate 20k and 30k (pay attention to sublevels in case you go over/under by a few k) - get 20k to reach level 84.
From level 130 to 140 and 140 to 150, get 50k at a time since it's faster not to go through the ramp animation,
We do this because you gain a noticeable speed boost on every level multiple of 10.
NOTE: You can also use space buffering in flying, it's just harder since you need to angle yourself to hit the correct score (20k, 25k, etc.) well in advance since you need to be holding nothing but space for about half a second before dying).
https://imgur.com/vjOmLsB~~

This is all really outdated (and incorrect). A few days after this guide was last updated (in January 2021), UnrealArchon analytically determined the optimal flying strategy. You can find the full document on the discord. However, we lately discovered that there are (extremely minor) improvements over that original model.

In short, for flying, a relatively fast strategy (and UnrealArchon's original proposal) is to spend exactly 6.22 seconds (including ramp time) on each cycle. Simplified, this leads to the following route:
Flying 1: 18k, then 19k until you reach 84.
Flying 2: 30k, then 31k four times, then 32k three times or until you hit 150.

The document also explains how effects such as the speedup every 10th level do not actually exist, so just follow this route and you'll be losing a very minimal amount of time in flying overall. Space buffering should still be used.

'Menu' (pre-position).
'Enter Race'.
Click 'Expert Races'
3-2.
SS (Stop as soon as your swimming level hits 146, since you can beat the champ with 150/146/150).

Flying 2 (5000 points per level):
Get to level 150 in groups of 10, exactly the same as Flying 1 but faster.

'Menu' (pre-position).
'Enter Race'.
Tab Space.
1-2.
'Enter Race' (pre-position).
Click 'Beginner Races'.
1-4.
'Enter Race' (pre-position).
Click 'Amateur Races'.
2-4.
'Enter Race' (pre-position).
Click 'Expert Races'.
3-4.
'Enter Race' (pre-position).
Click 'World Championship'.
'Skip'.

Done.

Remember to Tab Enter out of every race.
You need to collect approximately 100 coins throughout the run to reach swimming 146 (assuming you get 92 in Swimming 1).

SHORT VERSION (For reference during runs):
Running 44+
1-1
2-1
SS
Swimming 89+
1-3
2-3
SS
Running 110-115 (113 is fairly safe)
3-1
SS
3-3
SS
2-2
SS
Flying 84
3-2
SS
Flying 150
1-2
1-4
2-4
3-4
Champ