From your description of your data I imply that there are two consecutive commas in each line, either after field 3 or before field 4. You could just s/,,/,/; on each line.

Update: While you are at it you could also add quotes around the remaining commas and print the line:

while(<INFILE1>) {
  chomp;
  s/,,/,/;
  s/,/","/g;
  print OUTFILE1 "\"$coid\",\"$_\"\n";
}
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