That flip flop solution looks like it may work out pretty well for me.

my $infile = <STDIN>;
print"Your input file is $infile\n\n";
my $outfile = "out.log";
open (INFILE, "<$infile")||die "no such file";
open (LOG, ">$outfile")||die "no such file";

while (<INFILE>) {
    if (/^Begin Targets/ .. /^End Targets/) {
        next unless /^\d/;
        push @data, [split /\s/];
    }
    count++;
}
[download]

Im back on my way, thanks!