I see other problems in your code:

• You don't use placeholders in the SQL statement.
• You don't use prepare_cached().
• You try to implement your own quoting.
• The quoting code can be circumvented (just make $word[$count] false, e.g. by inserting " 0" into a line in the input file), which leads to a SQL injection vulnerability (all words following the 0 are not modified at all). Don't loop over the first few elements that are true, loop over all elements (foreach (@word) instead of while ($word[$count])).
• You don't reset $count to 0 before the for loop, it still contains the number of non-false "words" at the beginning of the last line read. So you start filling @data at some unknown offset, and all elements of @data up to that offset are undef.

  next if !defined ($string);   # should never be true.
  [download]

  even shows that you are partly aware of that problem. Change next to die "should not happen" and see your script die.
• You mess with $count and arrays where a simple push would be sufficient. Don't make your life harder then necessary by trying to write C in Perl. Get rid of $count in the for loop, use push @data instead.

See also Re^2: Massive Memory Leak and Re: Counting rows Sqlite for the first three points.

Alexander