(Disclaimer: I didn't DV or VTC this question.)
I think you probably have a decent question buried in there, but it's hard to get through reading the whole post and understanding your point. Because your post isn't very clear and direct, maybe voters couldn't get what you were asking and voted to close as unclear because it was unclear to them. (This possibility is borne out by Valorum's criticisms and suggestions in his answer on this meta.) Let's not get into whether or not these are good reasons to VTC, and instead focus on what you're asking: how to improve the post for reopening.
For readability of your posts, I suggest you try to make more use of
formatting tricks. It may not sound important, but judicious use of lists, bullet points, occasional bold text, etc. can really help to make a post
flow, to make it easier to read and easier to understand.
I'll admit that even I haven't read your whole post in full detail, but it seems that you're asking about the Hogwarts elective classes, providing a lot of evidence for why the scheduling doesn't seem to make sense, and asking if there's any way to understand it so that it actually makes sense. Here's my suggestion for how to reorganise the question so that it itself makes more sense:
Start by summarising the topic. Your first few paragraphs, down to "The difficulty here is that the scheduling system doesn't seem to work out.", already do a fairly good job of this: you introduce "elective courses" with some quotes and then list them all before coming to your main point about the scheduling system. The purpose of this section should be to make clear what you're asking about and what you're going to ask.
Summarise your evidence in an easy-to-read manner. The next section of your question, especially the really long paragraphs, is where my eyes glazed over when reading it. These parts really needs to be streamlined, perhaps using a bullet-pointed list and putting some main points in bold text. Lots of evidence is good, but it's also good to be able to glance over the question and get at least some of the main ideas. You've got lots of different pieces of evidence for why the scheduling doesn't make sense? Split 'em up, list 'em clearly, and try to summarise each one with a brief sentence in bold. That way someone who doesn't want to read every last word can at least get the essentials at a glance.
Finish up with a TL;DR of your question. You've already done this with your bold paragraph at the end, so that's fine. Really it's the middle bit that needs most work.
You can also use <hr> to draw horizontal lines between those three parts of your post, which again helps to visually split up the post and improve readability.
Of course, you can say that people who can't be bothered to read the whole question should simply skip it instead of reaching for the close button. Which is true. But just like we close/delete unreadable "walls of text" that contain no clear question inside them, people might be putting this post in the same kind of category. Sometimes you have to deal with the internet as it is rather than as it should be.
Of course this whole answer is just suggestions. The diamond gives me no extra authority here; I'm just giving you some advice on my personal behalf, which would definitely (IMO) help you to improve the question but wouldn't guarantee getting it reopened. You can take it or leave it.
Finally, since this is meta, I've employed lots of formatting tricks in this very answer to demonstrate my point. I'm guessing you'll get the point of this answer more quickly than if I'd just written several paragraphs of text with no emphasis, sections, or lists.
