Any advice to fix this plot structure and make it flow together better? It’s not finished, but this will be the general plot

I mean I'm not familiar with dan harmon's craft tips but they're always useful as an idea for structure rather than hard and fast rules.
Also for "getting what you want and paying for it" you can use it as a way to make sure your plot is never stagnant because you achieve one goal while creating your next conflict so they are logical together. I can't remember who I'm quoting but I remember a storywriting seminar where the speaker said:

"Write down all your story beats using connectors. If any of your story beats are connected by then or and you're f*cked. All story beats should be connected by therefore or but."

Basically trying to say that every story beat should flow logically from the next or be a catalyst for conflict with the previous beat.

Taken in that light, for your examples about "when do these people get what they want and pay for it?":

• Luke becomes a jedi but loses his mentor / finds the secret of his past but finds out his dad's in the big evil team

• Harry Potter finds out he's a famous wizard that people want to be around when he used to be mistreated and despised but finds out everyone wants a bit of his fame for themselves and most adults around him still treat him like an object

• Aang finds the air nomads he was looking for but finds out that they're all dead and he's alone.

There are so many examples like this because this is how conflict is made and built. After each of these the characters react and do things that they wouldn't have done had there not been the "but" statements, even in basic scenarios in almost every genre:

• the heroine falls in love, but her love interest already has a partner → CONFLICT

• the orphan wants to find out about their past but they find out their parents were horrible people and would rather have never known → CONFLICT

• the MC tells their deepest darkest secret to someone they trust to finally be free of the lie they've been carrying but that person doesn't accept them afterwards now they know → CONFLICT

• the MC finally kills their archenemy to be at peace but that archenemy had friends who want to avenge their death → CONFLICT

See how a ton of these are generic but also make logical sense and could easily be interesting when used well in a story?

That's because no every story structure applies to every story. They're not one size fits all. One could argue that for example, Zuko returns to how he was before he got obsessed with finding the Avatar, but that's really not important because not every story will fit every structure. They fit whatever structure the writers used. These are also no templates and shouldn't be considered such. They're rough ideas based on trends and commonalities. And most of the examples you listed at the top do get what they want (basically all of them being some kind of save the world and return home) and pay for it (usually with a lot of lives).

As for your actual plot, a lot of this is going to end up dependant on what sort of vibe you're going for, how fast you want your pacing and, unfortunately, the executation. You need to look at lots of different story structures and stories and how they pull them off and work out what works best for you. Unfortuntely, or fortunately depending on you view, a lot of research for creating is looking at and studying other people's creations and trying to figure out what works and what doesn't. I find serious book reviews essays on youtube quite useful for this as they talk a lot about things like structure and pacing.

Assuming that the world suffering because of the dark lord isn't related to the what's happening with the king, that shouldn't be there. It might be where you're showing it in the plot, but it's world building, not an actual plot point. If anything I'd think that it's more like "the wold is suffering because of the dark lord and so the king tells his son..." unless that was for some other reason, but it seems logical to me that you want a chosen one, fake or otherwise, because of the dark lord, not the other way around.

Ok, I think I get what you're struggling with there. For a start, Emmet probably has his own internal logic. The logic of what we do things doesn't always work in order, in fact it often works backwards. Plot overall should follow "action then consequence" but people tend to work in "preparation then action". Think about any human's morning routine, they are going to work so they do these things. Emmet does these things so he can go to work. But, those are also smaller scenes, not plot points. It would be much more accurate from a plot perspective to say Emmet was living a normal life until which is also perfectly valid. Therefore and so are not the only connections, but they make it clear that one thing is connected to another. A character brushing their teeth doesn't need to impact the plot, nor some greater reason to do so, but a character doing something like killing someone probably does.

As a general rule, cause and effect keeps the story ground. Something that comes out of nowhere for no reason is generally considered a plot contrivance or deus ex machina. Worlds general work on cause and effect, logical consistency, you know? However, plot and narrative can be different. For instance, if you're telling a non-linear plot, it might not be presented as action then consequence. You might see the consequence before the action, but it will still have been an action then a consequence. In the same way prologues about who the world was created don't necessarily lead directly to the plot, but will have somehow affected it.

And again, it's things like overall plot structure more than scene to scene. Things like LOTR, the prolgoue doesn't directly lead to the next scene. It's not because the ring wasn't destroyed so we can have a party . It's because the ring was not destroyed, the ring is in Bilbo's possession so it can be passed on so it can be destroyed.

"Most stories don't have that kind of a moment" They do. The reason it happens over and over again is because the price they pay for getting what they want will change what they want. It happens a lot, gaining importance until the final act where they're sure they want this thing and they get it.

For the "returning to what is familiar to them" it's similar to the return home in the hero's journey. It's used to highlight how far the character's come because back with a familiar élément you can contrast to see what's changed. Zuko does go back to the fire nation that's been his home for most of his life, but changes it for the better. Shrek goes back to the swamp with friends, etc...

I think instead of just looking at the craft tips you're given and questioning them on the surface, try understanding what those tips are getting at. Usually craft tips are giving you some slightly easier to grasp examples of using contrast to highlight change, creating conflict to get tension in the story, give readers a reason to feel something about your characters, etc...

The specifics of craft book structure will not apply to every story, but the spirit will, so you need to work to understand the spirit of the tip and apply it to your story.

To apply the therefore/but idea to what you've said you need to boil down to core motivations and essentials.

• Heiroe is told a fundalental lie that his life has a purpose (presumably to kill Bad guy) by the king who he trusts

SO

• He mistrusts his family and other people generally and feels a loss of purpose. (Feeling bad for everything done wrong doesn't immediately track with feeling betrayed).

BUT

• BIG BAD that he thought he was supposed to beat is making people suffer

SO

• He finds a new purpose in life to find the "real chosen one"

SO

• He has to learn to trust others because this is a task he can't do alone

SO

• While growing as a person he gains new friends and New values in his life and no longer feels guilt for not achieving the King's impossible standards

SO

• With the help of the team he finds the actual chosen one (what he wanted)

BUT

• Chosen one doesn't want to do it? / Turns out Heiroe was rhe chosen one all along? / Finding the chosen one reawakens some jealousy or mental anguish from the King's betrayal? →MORE CONFLICT

SO

• The team have to find a way to convince the chosen one to come with them / get Heiroe to be good enough to fight big bad / get chosen one where he needs to go while dealing with Heiroe's emotional crisis

Etc etc ..

Side-note but IMO this seems like a parody name even when I read your first few pages... Especially as you've got a chosen one story which are very overused tropes therefore they're often used for laughs and genre satire. Like yeah he's the heir and the hero but it seems really on the nose, like if a secretly traitor character was called Liar McBad. The names of all the characters all come in to make the story feel really generic. I get some japanese anime do this but it's usually in a foreign language for the intended primary audience and also actually gags (Dragon ball comes to mind). Aang is not called "Saayvior" and Zuko isn't called "Firebad".

I accidentally hit send half way through don't mind me

I would simplify it and first try to focus on one character.
Heiroe or Nobody.
And tell the story from that perspective with minimum other characters
and then build the story from that.
And then write a summary of the story with understandable goals
with a plot that makes sense.

You can still add the other characters but I think you need a good
fundamental story that makes sense and works

There's a diference between a characters want and need. A want is what a character thinks they need, but generally a basic heroes journey will have a character evolve to the point where they realise they don't need their want and that's when they achieve their need.

Take the latest Puss in Boots movie. Goldilocks wants the wishing star to wish her family back. Everything she does is in purpose of that single goal, but in the end she realized she already had a family with the 3 bears. She needed to accept she already had what she wanted.

Same with Puss, he wanted more lives to he a courageous hero again, bu he needed to learn courage comes from facing fear, not the lack of it