05 V6 Hellion

2 Things come to mind. I have an 05 V6 Manual. I have noticed that while driving on the highway for prolonged periods of time, that when I would stop at the end of the off ramp and try to take off again, the car would shutter and nearly stall. From the research that I found, there is a TSB referring to a faulty fuel pump. Apparently air bubbles form around the fuel pumps inlet and these bubbles are injested, causing a shutter. It sounds similar to your problem. You might try looking into that TSB.

Also, in regards to the high idle when in neutral when the clutch is released, my car does the same thing. I also found a TSB regarding this and from what I understand, it is a simple programming issue. I haven't felt that this is something for me to worry about and just live with it.

Not sure if I am right, just my 2 cents! Good Luck!

SamInCleveland

Update:
It ended up needing a software update from Ford. The mechanic that maintains our trucks at work found the update and installed it and it's been running great for a month now.