Usually reading and writing CSV-files is best done with Text::CSV, but am I right in assuming that it is rather the parsing of the original data that is bothering you?

A couple of things,
• using <code> tags makes you code more legible without us having to inspect the source. You had to preview before creation, so how did you fail to notice that it was illegible
• you can either roll your own parser using something like

  open (INPUT, "<", "input.txt");
  while (<INPUT>){
     chomp(my $record = $_);
     print join ",", (split /\t/, $record);
  }
  [download]

  or use an existing module such as Text::CSV set sep_char to tab and let the module do the heavy lifting. This has several advantages over rolling your own in most instances, but given the data-set you should get away with the above capture style in this instance.

With your lack of <code>...</code> tags and other extremely poor formatting, I won't spend much time trying to figure out your question, I'm afraid, since it's easy for you to rectify. I will, however, suggest you Super Search for parsing, munging, and/or take a look at how Corion splits files based on columns.

It seems you need to understand text parsing. Simply stated, your script assumes one space and a dozen spaces are the same. Obviously this is wrong, and you need to account for each column of data in a hard format.

Whether learning Perl to solve this particular problem is the path to your solution only you can answer. I'm not totally familiar with AWK's full set of features, but I do know there are some fine columnar tools in 'cut'.