my @files = qw(File1.txt File2.txt);
my %tree;
my(@iterations, @names);  # order
foreach my $file (qw(File1.txt File2.txt)) {
    open my $fh, '<', $file or die "Cannot open file $file: $!";
    (my $name = $file) =~ s/\.\w+$//;  # remove extension
    push @refs, $ref;  # order
    my($iteration);
    while(<$fh>) {
        chomp;
        if(/^Iteration /) {
            $iteration = $_;
            push @iterations, $iteration unless $tree{$iteration};  # key order
        } elsif(my($i) = /^(\d+):/) {
            $tree{$iteration}[$i]{$name} = $_;
        }
    }
}

##</code><code>##

use Data::Dumper;
print Dumper \%tree;

##</code><code>##

foreach my $iteration (@iterations) {
    print "$iteration\n";  # section header
    my $section = $tree{$iteration};  # array ref
    for my $i (0 .. $#$section) {
        my @data;
        foreach my $name (@names) {
            my $data = $section->[$i]{$name};
            next unless defined $data;
            push @data, "$name:$data";
        }
        if(@data) {
            my $line = join " ", @data;
            print "$line\n";
        }
    }
}