I was able to get that output by changing the script like:

print $file $_ if s/$LeftSide/$RightSide/eegi;
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And then left side is just a comma ',' without the quotes and right side is "\n" WITH the quotes

EDIT: Using above little snippet, Use left side as \),\( and right side as "\)\n\(". And from what I understand the above snippet is the same as doing:

print $_ if s/$LeftSide/eval $RightSide/egi;
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So I also suggest reading PerlDoc: eval.

Heres another more hackish way to get the job done haha:

Create your main script like so, with keywords in the s///

# main.pl

# all this is just a template that creates "run.pl"
use strict;
use warnings;

while(<DATA>){    
    print $_ if s/search_here/replace_here/gi;
}

__DATA__
(123),(456),(789)
(abc),(def),(ghi)
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Then this following script will search and replace the keywords "search_here" and "replace_here" in the script above, with whatever you input and put it in "run.pl"!

# prepare_run.pl

open my $file, '+<', 'main.pl'; #your original script we will replace 
+keywords
open my $run, '+>', 'run.pl'; #newly created script that we will execu
+te below

print "Enter left side of s///: ";
chomp(my $LeftSide = <STDIN>);

print "Enter right side of s///: ";
chomp(my $RightSide = <STDIN>);

while(my $line = <$file>){
print $run $line if $line !~ /.*search_here.*/ || /.*replace_here.*/;
print $run $line if $line =~ s/(.*)search_here(.*)/$1$LeftSide$2/ &&  
+   $line =~ s/(.*)replace_here(.*)/$1$RightSide$2/;
}

close($file);
close($run);

system("run.pl"); #or whatever the the equivalent of your OS.
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Here is the script that the above will create and run:

# run.pl, will be created after running "prepare_run.pl" while using "
+main.pl" as a template.

use strict;
use warnings;

while(<DATA>){    
    print $_ if s/\),\(/\)\n\(/gi;
}

__DATA__
(123),(456),(789)
(abc),(def),(ghi)
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Download all the above and then just run "prepare_run.pl" and it will copy lines from main.pl while replacing keywords with your regex from STDIN and put it all in run.pl for execution. You can use \),\( and \)\n\( for STDIN per normal without using any quotes.

Here is the output:

(123)
(456)
(789)
(abc)
(def)
(ghi)
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