French usually don’t like repetition so using twice chacun is probably not the best solution.
You can use the formulation “tous les deux” or “tous deux”, which better translate in english to “both”. If there were three people, “each” would translate to “tous les trois” (ou “tous trois”).

Note : “tous deux” and “tous trois” are uncommon, mostly seen in litterature.

Cheers,
K.

“Each” can have 2 differents meaning in French:

• “Chacun” as you said
• “Tout les deux” or “Tous deux”

So in your sentence, the first translate of each is appropriate, but for the second, you should use “tous deux”, so the sentence will be :

Je pensais vraiment que Dan et Mary formaient un couple idéal. Mais ils
se sont chacun rendu compte de leur sentiment seulement après qu’ils
s’étaient tous deux mariés.

While your phrasing is perfectly understandable, there’s room for improvement to make it sound more idiomatic. How about:

Moi qui pensais que Dan et Marie formaient un couple de rêve. Mais ils n’ont réalisé leurs sentiments l’un pour l’autre qu’après s’être mariés chacun de leur côté.

I’d avoid repeating the word “chacun”:

In place of the 1st “chacun”, I’d use “l’un pour l’autre”, as the idea of “leurs sentiments (pour who/what?)” is lacking in your version.

As for the 2nd “chacun”, I’d substitute “chacun de leur côté”, thereby emphasising the idea that each of them ended up getting married “to a different partner”.

As an aside: You can also say “ils étaient faits l’un pour l’autre” to express the idea of “a perfect couple”. But to avoid repeating the phrase “l’un pour l’autre”, I’d go for “ils formaient un couple de rêve” or “ils faisaient un couple bien assorti”.