#!/usr/bin/perl
use strict;
use warnings;

while(<DATA>)
{
  next if /^\s*$/;                #skip blank lines
  s/^(\d+\s+)(\S+)(.+)/$1"$2"$3/; #quote column 2
  s/\s{3,7}/,/g;
  print;
}

=prints:
12345,"DOE,JOHN",$50.00,REFUND,COMPLETE
12345,"DOE,JOHN",$25.00,DENIED,COMPLETE
12345,"DOE,JOHN",$75.00,,COMPLETE
12345,"DOE,JOHN",$10.00,REFUND,COMPLETE
12345,"DOE,JOHN",,,INCOMPLETE
=cut

__DATA__

12345   DOE,JOHN   $50.00   REFUND   COMPLETE
12345   DOE,JOHN   $25.00   DENIED   COMPLETE
12345   DOE,JOHN   $75.00            COMPLETE
12345   DOE,JOHN   $10.00   REFUND   COMPLETE
12345   DOE,JOHN                     INCOMPLETE