You are right. Here is a version that saves the keys:

%my_array=(Key_One=>["50","25","100","90"],
  Key_Two=>["35","18","110","72"],
  Key_Three=>["100","35","99","82"]
);
$a_key = each %my_array;
for $column (0 .. $#{$my_array{$a_key}}) {
    @a = sort { $b->[0] <=> $a->[0] }
        map { [$my_array{$_}[$column], $_] } keys %my_array;
    print $column+1, ": $a[0][1]=$a[0][0], $a[1][1]=$a[1][0] \n";
}
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