I guess you are looking for something like this:

#!usr/bin/perl
use strict;
use warnings;
use 5.010;

my %data;

# Parse data
while (<DATA>) {
    chomp;

    my ($key, @chunks) = /(\w+ (?:\([^)]*\))?) (?: \s+ |$)/gx;

    next if !@chunks;

    foreach my $chunk (@chunks) {
        my ($prefix, $num, $tail) = $chunk =~ /^([a-z0-9]+)_(\d+)(.*)/
+i;
        $data{$key}{$prefix}{$num} = $tail;
    }
}

# Create lists of values
for my $key (keys %data) {
    for my $prefix (keys %{$data{$key}}) {
        my @items =
            map  {"${prefix}_$_$data{$key}{$prefix}{$_}"}
            sort {$a <=> $b} keys %{$data{$key}{$prefix}};
        $data{$key}{$prefix} = \@items;
    }
}

# Generate output
for my $key (sort keys %data) {
    my @prefixes = sort keys %{$data{$key}};
    my @lines;
    my @colMax;

    while (1) {
        my @items = ($key, map {shift @{$data{$key}{$_}}} @prefixes);

        last if 1 >= grep {defined} @items;
        $_ //= '    -' for @items;
        push @lines, \@items;
    }

    for my $line (@lines) {
        for my $colIndex (0 .. $#$line) {
            my $itemWidth = length $line->[$colIndex];
            $colMax[$colIndex] = $itemWidth
                if !$colMax[$colIndex] || $itemWidth > $colMax[$colInd
+ex];
        }
    }

    for my $line (@lines) {
        $line->[$_] = sprintf '%-*s', $colMax[$_], $line->[$_]
            for 0 .. $#$line;
    }

    print "@$_\n" for @lines;
}

__DATA__
ClusterX  a_123(something) b_675(some_other_thing) b_234(something new
+) c_897(some different thing)
ClusterY   b_6998(some_other_thing, thats new) c_877797(something diff
+erent inside here) c_111(some other different thing)
ClusterZ a_1234(something interesting) a_123467(something - else thats
+ is - interesting) 3850-1-2_12243(a new one)  3850-1-2_1789(another n
+ew one)
[download]

Prints:

ClusterX a_123(something) b_234(something new)    c_897(some different
+ thing)
ClusterX     -            b_675(some_other_thing)     -               
+       
ClusterY b_6998(some_other_thing, thats new) c_111(some other differen
+t thing)        
ClusterY     -                               c_877797(something differ
+ent inside here)
ClusterZ 2_1789(another new one) a_1234(something interesting)        
+            
ClusterZ 2_12243(a new one)      a_123467(something - else thats is - 
+interesting)
[download]

although the final "empty" ClusterZ line is not generated.

---

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