Contour Enthusiasts Group Archives Forums Modifications 3.0L Duratec Driveability woes (please help)

Well, then I can tell you that there is no issue with leakage past the secondary throttle plates into the engine. That isn't going to affect vacuum at all. If you mean the gasket between the LIM and the head or the UIM/LIM then yes and that is the first thing I'd check along with the injector Orings.
As long as you are running stock SVT PCM,INJ/MAF:
-should be no issue with fuel delivery

If that is the case then you need to check the upstream O2 sensors. The reason I say that is that your LT fuel trims are +17, not too far off but could be indicating a vacuum leak.

If you are counting say X cfm of air with the MAF, the pcm adds the correct amount of fuel. Lets say that with the vacuum leak there is an additional 5% air leaking in. So the O2 sensors would be switching more or less lean and the pcm would continue to add fuel to bring it up to the stoichiometric.
This would mean that the LTFT=+5% just compensate for the additional air above the maf counts that is coming from the vacuum leak.

The MAF nor the engine doesn't care if the air is flowing through the primary intake runner or the secondary intake runner, as long as the air that is counted by the maf is pulled into the cylinders then the pathway is not relevant at idle. Hopefully your IMRC is operating correctly though.

It doesn't necessarily have to be in the manifold but check it again for vacuum leaks. Check your PCV system and make sure the valve is the correct pcv for the contour/taurus engines. Check that the crankcase vent lines aren't vented to atmosphere. Check that there are no loose clamps on the intake ducting AFTER the MAF counts the air. Check your vacuum lines at the rear of the manifold, under the manifold at the Fuel pressure regulator too.
Did you plug off the oil return lines that the 3L head would have used on the block well enough? If you didn't and they are leaking that will be like having the crankcase vented to atmosphere and the PCV system will suck air that is unmetered by the MAF.
Lets not forget fuel pressure, is your pump in good shape and the pressure constant?

BTW, you should probably use your downstream O2s but put them back in with the addition of the MIL eliminator circuits. They provide an accurate check on the condition of the upstream O2 sensors. With the OBDII scan device you can look at them and they will switch just like before but will be lower in voltage and the amplitude of the switching will be lower. IF both sensors are operating correctly then the downstream O2 sensor with the MIL eliminator installed will mimic it but just with a "littler" graph. This keeps the PCM happy but it tells you everything is good to go. If they are ever different then it can help you diagnose a problem.