my @tworows = split /[^\n]+\n[^[n]+\n/, $text;

##</code><code>##

s/((\w+).+\1.+\1.+)\n(.+)/something/

##</code><code>##


1. 
next; 
}

is the same as 

}

2. Don't make a copy of your row array to use it, just dereference it:

my @row1 = @{$row}; # not needed..

Just use $row->[$index] instead of $row1[$index]


3. drop all the extra parens
  join ';', @arr;
  push @arr, 'something';


4. it looks like you're using a numeric == to compare ascii fields like $row1[0] == $row2[0] when col 0 contains things like 'PF'. Use eq for these compares. You can't use == there.