check the voltage from the AFM - although you can't adjust for cat equiped cars.
Blue/red CO trim value 1.8 for cat cars
Blue/Green Air flow signal- should be .2-.7 volts (no air flow). Tick over on the 3.9 is about 1.7 volts
do you have the correct tune resitor for the ECU - should be Green 470 Ohms
You can adjust the MAF on a cat equipped car but because the ECU uses the input from lamdas it ignores the setting on the MAF and only responds to lamda and this is why it is often said you can't adjust if running cats.
The tune select resistor you mention above is for non-cat cars. The correct value for european catalyst cars is 3k9 Ohms and should have a white wire.