Čim se opet naoblači, moja baka zatvara prozore jer se boji tuče.

Čim means as soon as. It shows that one action happens immediately after another:

• Čim se opet naoblači, ... = As soon as it gets cloudy again, ...

Compared with kad (when), čim is more specific and more immediate.
So:

• Kad se naoblači... = When it gets cloudy...
• Čim se naoblači... = As soon as it gets cloudy...

In this sentence, čim is the better choice because the grandmother reacts right away.

Croatian often uses the present tense after time words like čim, especially for:

• future situations
• repeated/habitual situations

This sentence sounds like a general habit:

• Whenever / as soon as it gets cloudy again, my grandma closes the windows...

So the present tense here is very natural. English does something similar:

• As soon as it gets cloudy, she closes the windows.

If you wanted to emphasize one single future event, you could say:

• Čim se opet naoblači, moja baka će zatvoriti prozore.

Croatian does not need a dummy subject like English it in weather expressions.

English says:

• it gets cloudy
• it rains

Croatian can simply use the verb:

• naoblači se
• kiši / pada kiša

So there is no separate word for it here. The verb itself is enough.

Because naoblačiti se / naoblači se is a verb used with se. In this weather meaning, se is part of the verb expression.

It does not literally mean that something is doing the action to itself.
It is just how this verb works in Croatian.

So you should learn it as a whole unit:

• naoblači se = it gets cloudy / it clouds over

Without se, it would not sound like the normal weather expression.

Because bojati se is also a verb that normally comes with se.

So here you have two different verbs, and both require se:

• naoblači se
• boji se

Again, this is something you usually need to memorize with the verb.
A good habit is to learn Croatian verbs in their full form:

• bojati se = to be afraid
• nadati se = to hope
• sjećati se = to remember

Opet means again.

So:

• Čim se opet naoblači... = As soon as it gets cloudy again...

Its position is natural because se is a clitic, and Croatian clitics usually go very early in the clause.
That is why se comes before opet here.

The order:

• Čim se opet naoblači

sounds normal and neutral.

Moja baka is the subject of the main clause, so it is in the nominative case.

• moja = my
• baka = grandmother / grandma

Croatian has no articles, so there is no separate word for the or a.

That means moja baka can mean simply my grandmother / my grandma, without needing an article.

Because prozore is the direct object of zatvara, so it must be in the accusative plural.

• nominative plural: prozori = windows
• accusative plural: prozore = windows as the thing being closed

So:

• Prozori su otvoreni. = The windows are open.
  Here prozori is the subject.
• Baka zatvara prozore. = Grandma closes the windows.
  Here prozore is the object.

Because the verb bojati se takes the genitive case.

The noun is:

• nominative: tuča = hail

After bojati se, it becomes genitive singular:

• tuče

So:

• boji se tuče = is afraid of hail

This is a very common pattern in Croatian:

• bojati se psa = to be afraid of a dog
• bojati se mraka = to be afraid of the dark
• bojati se tuče = to be afraid of hail

Also, learners often notice that tuče looks like the verb form tuče (he/she hits). Here, though, it is clearly the noun tuča in the genitive.

Yes. Jer means because and introduces the reason:

• ... zatvara prozore jer se boji tuče.
• ... closes the windows because she is afraid of hail.

You could also say:

• ... zatvara prozore zato što se boji tuče.

Both are correct.
Very roughly:

• jer is shorter and very common
• zato što is also common and can sound a little more explicit

In this sentence, jer is perfectly natural.

Yes, Croatian word order is more flexible than English word order, but not completely free.

This sentence has a neutral, natural order:

• Čim se opet naoblači, moja baka zatvara prozore jer se boji tuče.

You can move some parts for emphasis, for example:

• Čim se opet naoblači, prozore zatvara moja baka...

But that sounds more marked or stylistic.

One important thing: clitics like se usually stay near the beginning of the clause, so you normally keep:

• Čim se opet naoblači
• jer se boji tuče

rather than moving se around freely.

Most naturally, it describes a habit or repeated behavior:

• Whenever it gets cloudy again, my grandma closes the windows because she is afraid of hail.

That is because both main verbs are in the present tense:

• naoblači se
• zatvara

So the sentence sounds like something she regularly does.

If you wanted one specific future event, Croatian would more often say:

• Čim se opet naoblači, moja baka će zatvoriti prozore jer se boji tuče.