Ворона летела над дорогой и села на дерево.

Because the subject, ворона (crow), is grammatically feminine.

In the past tense, Russian verbs agree with the subject in gender and number:

• masculine: летел
• feminine: летела
• neuter: летело
• plural: летели

So:

• ворона летела
• ворона села

both use the feminine past-tense form.

This is a very common Russian pattern: the sentence mixes imperfective and perfective because the two actions are viewed differently.

• летела = was flying / flew as an ongoing action
  This is imperfective.
• села = landed / perched as a completed single event
  This is perfective.

So the idea is:

• the crow was in the middle of flying
• then it completed the action of landing

That is why this combination sounds natural.

If you said Ворона летела над дорогой и садилась на дерево, it would sound odd in most contexts, because садилась suggests an ongoing or repeated attempt to sit/land, not one finished landing.

Because the preposition над usually takes the instrumental case when it means above / over.

The noun дорога changes like this:

• nominative: дорога
• instrumental: дорогой

So:

• над дорогой = over the road

This is just a case rule:

• над + instrumental

Examples:

• над домом = over the house
• над морем = over the sea
• над дорогой = over the road

Because Russian uses different cases after на depending on whether there is movement toward a place or location at a place.

• на + accusative = movement onto/to
• на + prepositional = location on/at

Here the crow landed onto the tree, so Russian uses movement:

• села на дерево

Compare:

• Ворона сидела на дереве = The crow was sitting in/on the tree.
• Ворона села на дерево = The crow landed on the tree.

So English often uses on in both cases, but Russian distinguishes them grammatically.

Good question. It is in the accusative, but for many inanimate neuter nouns, the accusative singular looks exactly like the nominative singular.

So:

• nominative: дерево
• accusative: дерево

That means the form does not visibly change, even though the case has changed.

Compare with location:

• на дерево = onto the tree (accusative)
• на дереве = on the tree / in the tree (prepositional)

So the case difference is real; it just happens that дерево has the same form in nominative and accusative.

Literally, yes: сесть / села is the verb to sit down.

But with birds, Russian often uses it in the sense of:

• landed
• perched
• settled on

So in this sentence, села на дерево is best understood as:

• landed on a tree
• or perched on a tree

This is very natural Russian.

Because both verbs have the same subject, and Russian does not need to repeat it.

So:

• Ворона летела над дорогой и села на дерево.

means:

• The crow was flying over the road and landed on a tree.

This works the same way in English:

• The crow was flying over the road and landed on a tree.

You usually would not repeat the crow unless you wanted special emphasis.

This word order is fairly neutral and natural:

• Ворона летела над дорогой и села на дерево.

Russian word order is flexible, though, because case endings show the grammatical roles. You could change the order for emphasis:

• Над дорогой летела ворона и села на дерево.
• На дерево села ворона, летевшая над дорогой.
  (more literary / more marked)

But the original sentence is a good straightforward default.

A natural stress pattern is:

• воро́на лете́ла над доро́гой и се́ла на де́рево

Approximate pronunciation:

• va-RO-na lye-TYE-la nad da-RO-goy ee SYE-la na DYE-ree-va

A few useful notes:

• е after a soft consonant often sounds like ye
• unstressed о is often pronounced closer to a
• ё is not written here, because these words do not contain ё

Yes, grammatically you could, but over the road is usually the more natural English translation here.

• над дорогой literally means above/over the road
• in normal English, for a bird in flight, over the road sounds more idiomatic

So:

• The crow was flying over the road...

is usually the best translation, even though above the road is not wrong literally.