Well, without seeing any PID data while the vehicle is running, what your describing sounds like maybe an O2 sensor. If everything is fine until the vehicle enters closed loop operation (first few minutes of running) chances are its not vacuum. Closed loop is when the PCM starts recognizing the input from the O2 and adjusting fuel trim, if the O2 is out of range the PCM can start starving the engine of fuel. Not saying that's it, but it is a likely suspect.