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As per the title, I'm looking for a shorter expression that has generally the same meaning as "something clicked".

Closest one I could think of was something like "enlightened", but that isn't too fitting for my needs, which is something like:

He was befuddled until he saw the instruction sheet, at which point everything clicked into place.

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    Just clicked is fine. – Azor Ahai Dec 24 '15 at 7:10
  • Agreed. Based on the title, I thought you were looking for something like "seated" (as in "fit into position"). – Greg Brown Dec 24 '15 at 13:09
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You have a number of metaphorical possibilities:

The light dawned. From The Bonevski Legacy by F Duerden:

     Mo looked confused, "I'm sorry, you're the?
     "Locum, the stand in for Reverend Meeches. I understand from the bishop may be absent from his duties today."
     Suddenly the light dawned for Mo. "So that's why there was no answer at the vicarage this morning.

Fell into place. From Encounters: People of Asian Descent in the Americas by R Rustomji-Kerns:

It was the way in which those words were spoken or heard that embodied the spirit of my father and all his peculiarities. In that moment of revelation everything fell into place. It finally made sense to me why my father used to address strangers as "my friend."

Crystalized. From Assassin on Stage: Brutus, Hamlet, and the Death of Lincoln by A Furtwangler

For him, as for Clarke, Booth's performances were a revelation; they suddenly crystalized the meaning of all poetry and drama and left a lifelong impression.

The fog cleared. From Don't Look Back: (Lily's Story, Book 2) by C Kersey

I was still by the back door where I had fallen, but Greta had stopped barking. At first I was groggy an couldn't remember exactly what had happened, but as the fog cleared from my mind, it all came back to me in stunning detail.

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My favourite idiom for this is: the penny dropped

used to indicate that someone has finally realized or understood something

This saves you an entire word: you replace "everything clicked into place" with "the penny dropped".

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You could also use "made sense" in this context, although it is not that much shorter.

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Consider,

everything became crystal clear.

crystal clear: very easy to understand CDO

the fog lifted from his mind

lift: to move upward and disappear or become scattered The haze lifted. M-W

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