Perhaps you have a problem with the staged injectors?  This would seem
   to fit with the throttle position behavior (comes & goes with throttle
   position).  Perhaps the EFI computer has the wrong setting for them
   (wrong rate, wrong duration), the wiring has a fault (insufficient
   current), the injector's fuel supply is compromised (fuel rail defect,
   o-ring mis-seated), or the injector is fouled (particulate obstruction,
   gumming)?

   I'm with Paul: see if you can measure mixture in the *exhaust* (use an
   O2 sensor and unleaded gas).  Since we seem to have ruled out air intake
   problems, measuring mixture will give an indication if fuel delivery is
   the problem.

Dave,
I would wonder about the fuel pressure regulator "going off" or
failing. If the regulator was having a problem or the lines were leaking
(manifold pressure line) you would have inadequate fuel pressure and the
mixture would  go lean.

Bill Jepson