It sounds to me like your EGR isn't operating, and you're probably getting the same error as those who blank it off with later ECUs.
With regards to the MAF, what sort of run did you do - you really need to do a full power run in 3rd or 4th right through the rev range, and look at actual vs. requested, to know if your MAF is reading correctly or not.
IIRC at low throttle and/or low engine speeds, there can be quite a big difference between actual & requested, which isn't necessarily an issue. It's the full power run you need to look at.
With regards to the MAF, what sort of run did you do - you really need to do a full power run in 3rd or 4th right through the rev range, and look at actual vs. requested, to know if your MAF is reading correctly or not.
IIRC at low throttle and/or low engine speeds, there can be quite a big difference between actual & requested, which isn't necessarily an issue. It's the full power run you need to look at.