In the first file, I basically store the data in a hash of array structure where I used 'Iteration...' as my key. When I loop through the second file, I would simply check if the key exists and if it does, then it should print the corresponding data.

#!/usr/bin/perl

use strict;

my $file1 = <<END_FILE2;
Iteration 1:
0: Data: 1023 1023
1: Data: 200 1023
2: Data: 300 1023
3: Data: 250 1023
4: Data: 1023 1023

Iteration 2:
0: Data: 1023 1024
1: Data: 1023 60
2: Data: 1023 90
3: Data: 1023 100
4: Data: 1023 1023
END_FILE2

my (%record, $key);

for my $i (\$file1) {
    open( my $file_1, '<', $i ) or die "cannot open file";
    while( <$file_1> ) {
        $key = $1 if ( s/^(Iteration \d\d?):// );
        push( @{ $record{$key} }, $1 ) if ( /(\d:\s.*)/ );
    }
    close( $file_1 );
}

while (my $line = <DATA>) {
    if ( $line =~ s/^(Iteration \d\d?):// ) {
        $key = $1;
        print "$key:\n";
    }
    my ($index) = $line =~ /^(\d)/;
    print "File1:$record{$key}->[$index] File2:$line" 
      if ( defined( $index ) );
    print "\n" if ( $index == $#{ $record{$key} } );

}

__DATA__
Iteration 1:
0: Data: 1023 1023
1: Data: 250 1023
2: Data: 60 1023
3: Data: 99 1023
4: Data: 1023 1023

Iteration 2:
0: Data: 1023 1024
1: Data: 1023 60
2: Data: 1023 90
3: Data: 1023 100
4: Data: 1023 1023
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