CM870 vibration and black smoke

[Mluper7]

So far I've replaced my turbo air control valve, cleaned my intake manifold pressure sensor, Intake manifold temp sensor, exhaust pressure sensor, and my EGR temp sensor. My EGR and EGR cooler are less than a year old and still fairly clean.
I took it to a dealership today to do a cylinder cut out test, turbo and EGR test and everything checked out. When we went through to cut each injector number 4 seemed a bit week. So we did a cut out test with one injector on and went through them all. They all seemed strong and had no stuttering or stalling issues.
My engine harness is pretty ragged so I bought a new one today and I'm going to install it in the morning. Every now and then when I turn my ignition on I'll get a check engine light, and my Road Relay will tell me "Intake manifold pressure sensor circuit, service soon. Voltage Normal".
My boost issues and black smoke didn't really get bad until I cleaned all my intake sensors. Since I've done all this trouble shooting my current status is no boost when idling. I'll start driving and will have 3 lbs of boost until I get onto the highway and pick up speed.
My engine clatters and now is surging when at high idle (1200 PRM). The truck will rock and surge for as long as it's in a high idle with no boost. Black smoke is still very heavy when I shift gears and mash on it.
When I go to install my engine harness in the morning I plan to rebuild and clean my metering actuators. An other suggestions fellas?