Excuse me, I copied that last email's directions from http://www.nuonce.net/bq-cd.php and it's very confusing. It is using BlueQuartz GUI for CentOS.
All you wanted was how to run mkisofs. So this is how I do it and it seems to work.
Assuming you copied the cd contents to "custom_cd" directory make sure .discinfo gets copied....
cd custom_cd change isolinux/isolinux.cfg adding console=ttyS0,38400,n8 to append statement
mkisofs -P CentOS \ -b isolinux/isolinux.bin \ -c isolinux/boot.cat \ -no-emul-boot \ -boot-load-size 4 \ -boot-info-table \ -r -J -T -o ../custom_cd.iso .
Custom_cd.iso is the name of the new ISO burn it to a CD!
HTH Gerald