Try replacing the foreach loop with a while loop and just loop through the file. Something like this:

open(PAGES, "<pages.txt") || die $!;
my @filenames;
my @titles;
my @headings;
my @xstuff;
while (<PAGES>){
    if (m/^\*{4}filename.ext\*{4}/) {
        s/^\*{4}filename.ext\*{4}//;
        chomp $_; 
        push(@filenames, $_);
    }elsif (m/^\*{4}title\*{4}/) {
        s/^\*{4}title\*{4}//;
        chomp $_;
        push(@titles, $_);
    }elsif (m/^\*{4}heading\*{4}/) {
        s/^\*{4}heading\*{4}//;
        chomp $_;
        push(@headings, $_);
    }else {
        push(@xstuff, $_);
    }
}
  close PAGES;
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$_.=($=+(6<<1));print(chr(my$a=$_));$^H=$_+$_;$_=$^H;
print chr($_-39); # Easy but its ok.
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