Learn Hardcore Dutch: Zij had onlangs koorts, maar nu is zij nauwelijks nog ziek. - She recently had a fever, but now she is hardly sick anymore.

nauwelijks nog = hardly anymore; the condition has almost faded.
nog = still/yet (neutral): Ze is nog ziek.
nog steeds = still (more emphatic/insistent).
niet meer = no longer (full negation): Ze is niet meer ziek.
nauwelijks (alone) = hardly: Ze is nauwelijks ziek (no “anymore” nuance).

Why is it had and not heeft … gehad?

Both are possible:

Zij had onlangs koorts (simple past) is common in writing/narration, especially with a time adverb like onlangs.
Zij heeft onlangs koorts gehad (present perfect) is very common in speech. Meaning is effectively the same here; it’s a style/variety preference.

Why Zij and not ze?

zij is the stressed form (emphasis/contrast), ze is the unstressed everyday form.
Repeating zij adds slight emphasis: … maar nu is zij …
Very natural alternative: Ze had onlangs koorts, maar nu is ze nauwelijks nog ziek.

Why is it maar nu is zij and not maar nu zij is?

Dutch main clauses follow the V2 rule (finite verb in second position). If you start with an adverb like nu, the verb comes next:

Maar nu is zij …
If the subject comes first, you can say: Maar zij is nu … (also correct).

Where can onlangs go, and are there synonyms?

Positions: Zij had onlangs koorts; Onlangs had zij koorts (both natural). Zij had koorts onlangs sounds off.
Synonyms: recent, recentelijk (formal), kort geleden (neutral), laatst (colloquial/regional), pas (colloquial; can also mean only, so be careful with ambiguity).

Why no article before koorts? In English we say “a fever.”

koorts is generally uncountable in Dutch and used in the fixed expression koorts hebben.
No article: Zij had koorts.
Use an article only for named/specific fevers: de gele koorts (yellow fever). De koorts for a particular episode is unusual in modern everyday Dutch.

Is there a difference between nauwelijks nog and nog nauwelijks?

Yes:

nauwelijks nog = hardly anymore (declining state): Ze is nauwelijks nog ziek.
nog nauwelijks = hardly yet (early stage): Ze is nog nauwelijks ziek (she’s only just starting to get sick, if at all).

Is the comma before maar required?

It’s optional but common to separate two independent clauses: …, maar ….
Without the comma is also acceptable in many style guides.

Could zij mean they here?

No. The verb form shows it’s singular:

Zij had = she had.
Zij hadden = they had.

What are natural alternative ways to say this?

Ze heeft onlangs koorts gehad, maar nu is ze nauwelijks meer ziek.
Ze had laatst koorts, maar nu is ze amper nog ziek.
Onlangs had ze koorts, maar nu is ze niet meer erg ziek. All keep the same idea; amper and nauwelijks are near-synonyms, and meer can replace nog for the “anymore” meaning.

Can I use koortsig instead of koorts?

koortsig = feverish (adjective): Zij was koortsig / Zij voelde zich koortsig.
koorts hebben is the standard way to say someone has a fever; koortsig focuses on how she felt.
Mild fever: verhoging (slightly elevated temperature).

Where does nog usually go in sentences like this?

For the “anymore” meaning with a minimizer, put nog after the minimizer: Ze is nauwelijks nog ziek or use meer: Ze is nauwelijks meer ziek.
Nog nauwelijks yields the “hardly yet” meaning (different timeline).

Pronunciation tips for tricky words?

zij: like English “z” + “eye”.
onlangs: roughly “ON-lahngs”.
koorts: long “o” and a final “ts”: “koorts”.
nauwelijks: roughly “NOW-wuh-luhks”.
maar: “maar” with a long “a”.
nog: short “o”, final consonant like a soft “kh” in many accents.

Is repeating zij in both clauses okay?

Yes. It’s fine to repeat, though many speakers would switch to the unstressed ze in the second clause: … maar nu is ze …. Dropping the subject entirely is not allowed in Dutch.

How would this look inside a subordinate clause?

With dat: Ik denk dat zij onlangs koorts had, maar dat zij nu nauwelijks nog ziek is. (finite verbs at the end of each dat-clause)
With hoewel: Hoewel zij onlangs koorts had, is zij nu nauwelijks nog ziek. (subordinate clause first; main clause keeps V2)