A tune file developed for 518 AF should work on the later 518 BC ECU hardware, so you should be able to cross flash the AF .bin file to your BC. (the 518 AK hardware and files - as used in the stage 1 community tune thread is also cross-flashable) .
However, note that in order to convert from auto to manual transmission, you also need to change the ECUs EEPROM file soft code to indicate that the car is now a manual.;
http://nefariousmotorsports.com/forum/index.php?topic=3449.0 (note that the EEPROM file needs a bench harness to change and re-flash, the reflash to the EEPROM cannot be performed through the cars OBDII port like is done for the main tune .bin file). Alternately, it is possible to change the soft code via the OBDII port using VCDS if you have it but do not have a bench harness.
If you instead want to use the 518 AF ECU hardware and have a bench harness, it is easy enough to read the SKC from your old ECU (matched to cluster), transfer that SKC to the replacement ECUs EEPROM so immobilizer works (or deactivate immobillizer on the new ECU). Note however that if you deactivate the immobilizer, you will not then be able to pair any new key transponders to the cluster so be sure you have all the keys that you will ever need before disabling the ECU immobilizer. (Car will run with the ECU immobilizer off, but cluster immobilizer will trip and flash hazzard lights, disable climate control while you drive!).
One other caution, if your new manual transmission is a 6-speed instead of 5-speed, there may be other complications with getting cruise control working with the 518 AF file.
