Thanks for the reply. I will need the full serial numbers of the engine and the machine to help you much further.
I have never had valve inserts leak. If they were loose, they fell out and were destroyed by the piston and that was the reason I made repairs.
I don't work in the dyno shop so, I can't tell you how the engine will respond on the dyno. I have not had this issue myself beyond fixing the air inlet as you have already done.
Here is a note about the FRC limits.
The personality module inside the ECM sets certain limits on the amount of fuel that can be injected. The FRC Limit is a limit that is based on the boost pressure. The boost pressure is calculated as the difference in pressure between atmospheric pressure and turbocharger outlet pressure. The FRC Limit is used to control the air/fuel ratio for control of emissions. When the ECM senses a higher boost pressure, the ECM increases the FRC Limit. A higher boost pressure indicates that there is more air in the cylinder. When the ECM increases the FRC Limit, the ECM allows more fuel into the cylinder.
Have you tried replacing the atmospheric pressure sensor? All pressure readings are based from this sensor's reading. If it reads too low, all pressures will be too low.
If you manual set the boost pressure by using shop air pressure, does the engine respond correctly? ( You said you tested the sensor this way, why not see if the engine will respond to the extra boost pressure?)
Please post the serial numbers so I can help you further.