In each recordline array:

• instances of @recordline[4], which reference the SO (journal source) column, need to be changed to @recordline[8].
• instances of @recordline[7], which reference the DT (document type) column, need to be changed to @recordline[11].
• instances of @recordline[14], which reference the CR (cited reference) column, need to be changed to @recordline[25].
• instances of @recordline[36], which reference the UT (ISI number) column, need to be changed to @recordline[50].

The full revised script is:

# PROCESS THE SECTION BELOW THE SCRIPT (BELOW THE  __DATA__ TOKEN)
# RECORD BY RECORD

# file handle for output to a file:
$outfile="./isioutrefs2004.txt";
open (OUTPUT, ">$outfile");

while ( <DATA> ) {
    # remove trailing record separator if found:
    chomp;
    # split line by tab delimiter and put the result in an array:
    @recordline=split (/\t/,$_);
    $fullrec=$_ ;
    chomp (@recordline[11]);
    while ( <DATA> ) {
        # remove trailing record separator if found:
        chomp;
        # split line by tab delimiter and put the result in an array:
        @recordline=split (/\t/,$_);
        $fullrec=$_ ;
        # save the isinumber -the 37th element under a separate variable
        $isinumber=@recordline[50];
        $publishedinjournal=@recordline[8];
        chomp (@recordline[11]);
        foreach (@recordline[25]) {
            $count++;
            @citedrefs=split /;/, $_;
            foreach (@citedrefs) {
                # do for each cited reference
                $countrefs++;
                @onecite=split /,/,$_;
                # add a line with running number, PubYear, #Title, and ISINumber to the output file
                print OUTPUT "$countrefs\t$onecite[1]\t$onecite[2]\t$isinumber\n";
                # this line just echoes some fields to the screen #as the script runs.
                # it may be commented out.
                print "$countrefs\t$onecite[1]\t$onecite[2]\t$isinumber\n";
            }
        }
    }
}
# the next two lines just echo some fields to the screen as the script finishes.
# they may be commented out.
print "Total Refs: $countrefs\n";
print "Total Number of Articles Authored/Co-Authored by MCW: $count";

# the data to be processed begins below the __DATA__ token.
__DATA__