When you duplicate the problem while on level ground accelerating/ romping on it? If you can duplicate it like that it does sound like you could have a cylinder misfire. To figure out which cylinder is misfiring you will need a scanner that would allow you to look at MOD6 data. You can try to rent one from your local parts store or buy one from like a place like Sears? I will attach some images from my phone.
With the advance scanner you will need to click on MOD6/ On-Board Monitoring and click on Test ID $53 Components $01-$06 are your cylinders 1-6 Notice value is 0. There is no misfire on this vehicle. If you see a value especially high that cylinder is misfiring. Try swapping spark plug with one cylinder with a value of 0 and click reset codes. That will start everything over and drive to create the problem. If value changes to where you moved the plug then spark plugs are no good. You can do the same thing with the wires and fuel injectors. If it does not change then I would suspect a faulty coil pack.
On a side not I have had issues with EGR ports plugging up. The 3.8L Windstar had that problem. One port would plug up and the you get too much EGR flow one one cylinder to make it miss. To eliminate that, unplug the EGR valve connector and try to duplicate. If problem is gone then the intake manifold needs to come off to clear out the ports. But as stated earlier I have seen that problem on the 3.8L Windstar and not on the 3.9L Freestyle. But just trying to throw some ideas. Good luck and let us know how you do.
Monday, October 17th, 2016 AT 5:36 PM