if there are mods that decrease pumping efficiency at idle (cams and stuff, cam timing, head porting etc) the stock pumping efficiency could make it seem like the injectors arent flowing what they are rated to do. restrictive return lines to the tank can do this too making the injectors seem larger than they are cause the fuel pressure is higher than normal.
an incorrect pumping efficiency value at idle could have you scaling the map based tables incorrectly to correct and then dialing the pumping efficiency in based on an incorrect injector size could have you chasing other tables that are now calibrated incorrectly.
id think about sending the injectors out for cleaning/flow testing.
or get a pump, regulator, and graduated cylinders and a stop watch and see what they really flow.
after setting the latency curve to what it should be based on the injector part number, FuelFullThrottle should be set up to the desired AFR values using the tools in MPTune and then PumpingEfficiency should be dialed in at WOT at the lowest attainable boost level.
that way you are measuring true pumping efficiency with the throttle plate wide open.
after i do that, almost everything else falls in line.
Brian