http://nefariousmotorsports.com/forum/index.php?topic=2973.0title=You have an ME7.1.1 ecu with immobilizer 3. The procedure for turning it off is in the above thread. You will have to use bootmode to write the eeprom, which can be done in the car so long as you put the ecu in bootmode first.
As for a 5 speed, you'll have to flash an S6 euro file, use appropriate softcoding (10612), and modify the file for a6 injectors and MAF.