Looking at the command line, it might be easier to not start with awk, but write perl from the start. This very much looks like a CSV data file, so you can use Text::CSV_XS and maybe this problem can be addressed using Spreadsheet::Read's xlsgrep and/or xlscat (both also grep CSV reliable)

The perl distribution comes with a a2p utility to convert awk code to perl:

$ echo '{out=$1;for (k=2;k<=NF;k++){out=sprintf("%s,%s",out,$k);}print
+ out}' | a2p | perltidy
#!/pro/bin/perl
eval 'exec /pro/bin/perl -S $0 ${1+"$@"}'
    if $running_under_some_shell;
# this emulates #! processing on NIH machines.
# (remove #! line above if indigestible)

eval '$' . $1 . '$2;' while $ARGV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shi
+ft;
# process any FOO=bar switches

$, = ' ';     # set output field separator
$\ = "\n";    # set output record separator

while (<>) {
    chomp;    # strip record separator
    @Fld = split (' ', $_, -1);
    $out = $Fld[(1) - 1];
    for ($k = 2; $k <= ($#Fld + 1); $k++) {
        $out = sprintf ('%s,%s', $out, $Fld[$k]);
        }
    print $out;
    }
$
[download]

From there on, you can modify to your hearts desire and include all other parts of your command line