Hon har också ont i fingrarna och axeln efter träningen.

Ha ont is the normal Swedish expression for to be in pain or to hurt.

So Hon har ont ... means She has pain ... / She hurts ... depending on how naturally you would say it in English.

Even though har literally means has, you should learn ha ont as a fixed expression:

• Jag har ont i ryggen. = My back hurts.
• Vi har ont i benen. = Our legs hurt.

In this sentence, ont is the form used in the expression ha ont. You do not change it to match the subject.

So you say:

• Jag har ont
• Hon har ont
• De har ont

You can think of ha ont as one chunk meaning be in pain. Even if you know that ont is historically related to the adjective ond, in everyday learning it is best to treat ha ont as a standard idiomatic pattern.

Swedish main clauses normally put the finite verb in the second position. Here the order is:

• Hon = subject
• har = finite verb
• också = also / too

So Hon har också ... is the natural word order.

This is very common in Swedish:

• Jag kommer också. = I’m coming too.
• De vill också följa med. = They also want to come along.

If you move också, the emphasis can change slightly.
For example, Hon har ont också is possible, but it sounds more like she hurts too with too added at the end for emphasis.

After ha ont, Swedish normally uses i before the place that hurts:

• ha ont i huvudet = have a headache / have pain in the head
• ha ont i ryggen = have pain in the back
• ha ont i fingrarna = have pain in the fingers

So i here works a lot like in in English: pain in the fingers, pain in the shoulder.

In coordinated phrases, Swedish often leaves out a repeated preposition if it would be the same:

• i fingrarna och axeln

This really means:

• i fingrarna och i axeln

Both are understandable, but leaving out the second i is normal and natural.

So the sentence means that she has pain in both places: the fingers and the shoulder.

Yes, literally they are definite forms:

• fingrarna = the fingers
• axeln = the shoulder

But with body parts, Swedish very often uses the definite form where English would use a possessive:

• Jag tvättar händerna. = I wash my hands.
• Hon har ont i ryggen. = She has pain in her back.
• Hon har ont i fingrarna och axeln. = She has pain in her fingers and shoulder.

So this is completely normal Swedish.

Because with body parts, the possessor is usually obvious from the context, so Swedish normally prefers the definite noun instead of a possessive.

So Swedish usually says:

• Hon har ont i fingrarna.

rather than:

• Hon har ont i sina fingrar.

Using sin/sina is possible in some contexts, but it often sounds more emphatic, contrastive, or less natural if the owner is already clear.

A good general rule is:

With body parts, Swedish often uses the + body part where English uses my/her/his + body part.

Because the sentence says she has pain in:

• the fingers = more than one finger
• the shoulder = one shoulder

So the grammar just reflects the meaning.

If both shoulders hurt, you could say:

• Hon har ont i fingrarna och axlarna.

Träningen is the definite form, so it means the training session / the workout.

In context, efter träningen usually means:

• after the workout
• after the training session
• after practice

It refers to a specific, understood event.

By contrast, efter träning can sound more general, more like:

• after training
• after exercise

So efter träningen is often used when speaker and listener know which workout or practice is meant.

It tells you when she has this pain: after the workout / after training.

So the structure is basically:

• Hon har också ont
• i fingrarna och axeln
• efter träningen

In natural English:

• She also has pain in her fingers and shoulder after the workout.

So efter träningen is an adverbial phrase of time/circumstance.

Yes. A few natural alternatives are possible, depending on emphasis:

• Hon har också ont i fingrarna och i axeln efter träningen.
  This repeats i for clarity.

• Efter träningen har hon också ont i fingrarna och axeln.
  This puts after the workout first. Swedish still keeps the verb in second position: har.

• Hon har ont i fingrarna och axeln också.
  This is possible, but the placement of också changes the emphasis slightly.

The original sentence is completely natural and straightforward.