Jag har ont i magen och halsen, så jag vill bara dricka te.

Swedish often expresses pain with ha ont, literally have pain.

So:

• Jag har ont i magen = I have a stomachache / My stomach hurts
• Jag har ont i halsen = I have a sore throat / My throat hurts

This is the normal everyday pattern for saying that something hurts.

Another common pattern is:

• Det gör ont = It hurts

So in this sentence, Jag har ont ... is completely natural Swedish.

Because Swedish usually uses the definite form for body parts in this kind of expression.

• en mage → magen
• en hals → halsen

So:

• ont i magen
• ont i halsen

This is very common when talking about your own body, especially when it is obvious whose body part you mean.

Because Swedish often prefers the definite form instead of a possessive with body parts when the owner is obvious.

A native English speaker might expect something like:

• i min mage
• i min hals

But Swedish normally says:

• i magen
• i halsen

This also happens in many other sentences:

• Jag tvättar händerna = I wash my hands
• Hon bröt armen = She broke her arm

Using min is possible, but it usually sounds more emphatic, contrastive, or less natural in ordinary conversation.

Because one preposition can cover both nouns when they are joined by och.

So:

• ont i magen och halsen

means the same as:

• ont i magen och i halsen

The version with only one i is very natural and efficient. Repeating i is also possible, but it is not necessary here.

Hals can mean either throat or neck, depending on context.

In this sentence, it clearly means throat, because:

• the person is talking about pain
• they only want to drink tea

That sounds like a sore throat, not neck pain.

If you want to be more specific, Swedish also has:

• strupe = throat/windpipe area, more anatomical
• nacke = the back of the neck

But in everyday Swedish, halsen often works just fine.

Here så means so or therefore.

It links the two ideas:

• Jag har ont i magen och halsen
• så jag vill bara dricka te

So the meaning is:

• I have pain in my stomach and throat, so I only want to drink tea.

It is a very common word in spoken and written Swedish.

Because så here is working like a coordinating link between two main clauses.

So Swedish keeps normal main-clause order:

• så jag vill bara dricka te

That is different from cases where a word like därför is placed first in the clause. Then Swedish usually has inversion:

• Därför vill jag bara dricka te

So:

• ..., så jag vill ... = normal after så
• Därför vill jag ... = inversion after fronted därför

Bara means only or just.

In:

• jag vill bara dricka te

it means that the only thing the speaker wants to do is drink tea.

So the sense is:

• I only want to drink tea
• I just want to drink tea

Its position before dricka is very natural in Swedish.

Because vill is a modal verb, and modal verbs are followed by the infinitive of another verb.

Here:

• vill = want
• dricka = drink

So:

• Jag vill dricka te = I want to drink tea

This is the same pattern as:

• Jag kan simma = I can swim
• Jag måste gå = I must go
• Jag ska äta = I am going to eat / I will eat

Because te is being used as a mass noun, in a general sense.

So:

• dricka te = drink tea

This is like English, where you also usually say drink tea, not drink a tea, unless you mean one serving.

If you mean one tea as an item, for example in a café, Swedish can say:

• ett te

But in this sentence, dricka te is the natural choice.

The comma is natural here because the sentence contains two coordinated clauses:

• Jag har ont i magen och halsen
• så jag vill bara dricka te

In modern Swedish, commas are often lighter than in English, so you may sometimes see similar sentences without one. But in a sentence of this length, the comma is perfectly normal and helps readability.

So the punctuation here is good standard written Swedish.