Сначала и она казалась виновной, но позже стало ясно, что она тоже невиновна.

Here и does not mean the conjunction and. It is a particle meaning also / too / even.

So и она means something like:

• she too
• even she

The idea is that she is being added to some previously mentioned group: others seemed guilty, and she did too.

Because и stands directly before она, it strongly highlights она.

Казалась is the past tense, singular, feminine form of казаться = to seem / to appear.

Why feminine? Because the subject is она, and in the past tense Russian singular verbs agree with gender:

• он казался
• она казалась
• оно казалось

The -сь is the reflexive ending, but with казаться it is just part of the normal dictionary form of the verb.

After казаться (to seem), Russian usually puts the predicate noun or adjective in the instrumental case.

So:

• она казалась виновной = she seemed guilty
• compare: он казался усталым = he seemed tired
• она казалась врачом = she seemed to be a doctor

That is why you get виновной (instrumental feminine singular), not виновная.

Стало ясно is a very common impersonal Russian expression meaning it became clear.

Literally, it is something like:

• стало = became
• ясно = clear

There is no explicit subject like it. Russian often uses this kind of impersonal construction where English uses a dummy subject:

• Стало ясно, что... = It became clear that...
• Было известно, что... = It was known that...
• Понятно, что... = It is clear that...

The form стало is neuter singular because that is the default form in this kind of impersonal past-tense structure.

Что introduces a subordinate clause and means that.

So:

• стало ясно, что она тоже невиновна

means:

• it became clear that she too was innocent

Everything after что explains what became clear.

This is a very common difference between Russian and English.

Russian does not usually do the same kind of tense backshifting that English does after a past-tense main clause.

So Russian can say:

• Стало ясно, что она невиновна.

Literally this is It became clear that she is innocent, but in natural English it is often translated as:

• It became clear that she was innocent.

In other words, Russian states the fact directly, without needing a past-tense was.

Also, in the present tense Russian normally has no overt verb "to be", so она невиновна already means she is innocent.

Невиновна is the short-form adjective, feminine singular, from невиновный.

Short-form adjectives are very common in predicate position when stating a condition, judgment, or status:

• он прав = he is right
• она готова = she is ready
• дверь закрыта = the door is closed
• она невиновна = she is innocent

Why not the other forms?

• невиновная is the full form and is more naturally used before a noun:
  невиновная женщина = an innocent woman
• невиновной would fit other constructions, for example after казаться:
  она казалась невиновной

So in this sentence, невиновна is the natural predicate form.

They are in different clauses, and their placement changes the emphasis.

• и она = she too / even she
  This strongly highlights она
• она тоже = she too
  This is a bit more neutral

So the sentence gives two separate ideas:

1. At first, she too seemed guilty
2. Later, it became clear that she too was innocent

Russian often uses particles like и and тоже very flexibly to control emphasis.

Yes. Russian word order is flexible, and changing it often changes emphasis more than basic meaning.

For example, you could also say:

• Сначала она тоже казалась виновной...

This is very natural and slightly more neutral.

The original:

• Сначала и она казалась виновной...

puts extra focus on она, as if to say she too / even she.

Likewise, она тоже невиновна is the normal order for she too is innocent. Moving тоже around is sometimes possible, but it can sound less natural or shift the focus.

So the given word order is mainly about emphasis, not a different core meaning.