The first thing which springs to mind for 'system too lean' is vacuum hoses & crank breather pipework. If they are broken / leaking and allowing fresh air in to the engine after the MAF it will cause the engine to run lean, and the ECU many not be able to compensate with fuel trim.
That might also explain the O2 sensor malfunction codes - if the ECU can't get the fuel trim in order it might conclude that the O2 sensors are giving bad data. I'm hypothesising there though.
Carb cleaner is a good way to detect vacuum leaks - spray it around hoses and joints, especially the crankcase breather plastic pipes. If the engine sucks any in it will cough for a moment.
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