Hi there! I wasn’t sure if I should post this under one particular grammar point because it’s more to do with: how they heck do you know when to use these separately?
Do they all mean the same thing? Is there nuance on when to use them?
[ないと] or [なくては] or [なければ] or the short form [なくちゃ].
There’s also the [べき] for must that I get a bit confused with when to use.
I apologize if there’s an existing answer. I searched around but I’m still lost.
My opinion is not worth much since I am not that experienced, but I will say it anyway. Worst case scenario is I am just plain wrong, and somebody will correct me xD So:
べき i would avoid as much possible. It is good enough you understand it when you hear or read it. Japanese culture does not like direct order, or being direct in general (that’s why they opt for HA more often than GA when speaking about themselves). It is rude in their view. That why they express “must” as double negation. “If you don’t do x, it will be not good” implies strongly enough that you mush or should do x.
As for first question as long as you follow associated grammar with each word there is not important enough difference. If you are not one those that believe your grammar must be as good as native if not better, then I do see a reason to be stress about it.
I don’t know if it is helpful. Somebody with more knowledge will for sure explain you specific differences soon 
EDIT: I will give you an example. I know for fact that there is some “important” difference between “must” and “have to” because I remember falling asleep on lesson explain it. But guest what? I never ever even once had problems because of not remembering what that difference is. And I used to live in UK for some time. I bet native speakers would have hard time explaining what that difference is.
If you are a native English speaker, use べき exactly the same way as ‘ought to’ (there is some moral responsibility to do it)
ならない is more for rules or even cultural type things, いけない is better for circumstances. However, don’t pay tooooo much attention to that, people do use them very interchangably. However いけない is almost always a better option if you don’t know which to use. (ならない）is better in books/writing.
So a quick overview of what I’ve gotten from reading and asking a couple native speakers:
いけない is more often spoken
ならない is more often written (or in very polite speech)
なくてはいけない is generic and can be used pretty much all the time
なければいけない can be spoken but usually only in politer speech (mostly because it’s really long)
なくちゃ(いけない) is a contraction and thus usually only used in informal situations (notice it’s short and doesn’t necessarily need the いけない)
ないと(いけない) similar to above is pretty common in speech because it’s short and also doesn’t necessarily need the いけない making it really easy to use in polite and informal speech
So overall, while there are technically slight usage differences, they are so small that to most people they are entirely interchangeable if you switch between いけない/いけません to match the politeness of the conversation (this doesn’t apply to the contracted forms which are only suitable for informal speech).
My recommendation, stick with いけない (or いけません in polite speech) paired with なくては or ないと until you get a better feeling for them all.
べき on the other hand, can be used to tell people what they can and can’t do but it’s almost never used this way. べき tends more to be used in the abstract (without being directly commanded to anyone in particular) to describe things we should or shouldn’t do as a society, people, member of a group, etc.
For example,
“We should ban nuclear weapons”
“People should give their seats to the elderly”
“People should wear a mask in public”
Are examples of where べき might be used.
I found sentence proving you right in my reading material:
つまりは…生徒が登校すべき時間ではない、ということ。
He does not say why we can think he should not be attending the school at that time (he meets nobody at entrance), but rather is implying it by make it a general statement about students like him (context: he is long late). And that is his personal narration so he is polite to himself i guess 