For many of the DTCs a CEL is not set until the fault occurs multiple times. That's to prevent excessive trips to the dealer for an occasional fault. There's a table in the tune that the PCM uses when it determines that the MAF sensor has failed. The PCM needs the airflow measurement to accurately calculate engine load. As I recall the PCM uses the TPS value and the engine RPM to estimate airflow when the MAF sensor has failed. I forgot that someone did your tune in person instead of remotely. I guess that you only have an AFR meter and a DTC reader which limits your instrumentation for troubleshooting. Did you upgrade your PCM to OBD II/EEC V? If so, I think there are some inexpensive OBD II monitors available with limited but useful datalogging capabilities. Have you reduced the fuel pressure since your tune was done because of the high flow pump? If so, that will lean the AFR which has a significant effect when the engine is idling after the cold start phase is complete.