The GT-R AFR monitors have long been incorrect in displaying the actual AFR as measured in the exhaust stream. Since the discrepancy was so large and the monitor could not be trusted at an early stage I adopted a different method of tuning the GT-R since it has a closed loop O2 feedback system at all times.
Generally when it comes to AFR there is an acceptable range for whatever motor you are running and the amount of airflow you are running through it. For example, you may be able to run between 11.2:1 and 11.8:1 with little to no effect on power output from the motor. Once you go over the limit for an acceptable AFR you will start to induce knock. Going too rich will net you a whole bunch of black smoke.
Assuming the above is true it was easy to set an AFR in the GT-R's target AFR map without knowing the exact AFR in the tailpipe. This is possible because of the closed loop O2 feedback system which is very good at achieving your target AFR from the low det map. Set it conservatively at first, in the lower range of what you would want it to run. If black smoke is pouring out the back of the car... its too rich.
Now you can log the AFR commanded and the A/F Alpha for both banks in order to dial in your scaling for injectors, load, multipliers and such. Once you have it nailed down for that commanded AFR you can go about your business in the rest of the tune and get that all squared away. The last thing you will want to come back to is your AFR. Now you can make small changes to the commanded AFR and check to see if leaning out the car is indeed producing power or just making it more knock prone.
AFR commanded is the number from the Low Det Fuel map. There are compensations which take place AFTER this which change the commanded AFR. These are unknown for the time being.
As a general rule the AFR commanded in the map seems to be at least .3-.4 richer than the actual Final Commanded AFR in the ECU. ie. 12.1:1 = 11.7:1 AFR.
Using the methodology above you can easily make the transition from and old AFR monitor to a new one. The AFR you have been commanding in the map will be the same, the AFR logged from the exhaust will be different, but your A/F Alpha will confirm the TRUE AFR instead of the incorrect one you have been used to.