Start with the obvious and have the PCM flashed with the 5.9 software. I would then want to see if I had any active codes and watch the O2 voltages in the data stream to see what's going on. Also check the cam/crank difference - anything more than 6 degrees either direction is a problem. What about the MAP, TPS and IAC numbers...are they in the normal operating range? Since you mentioned it runs lean, have you verified fuel pressure AND volume?