2014 Fusion lean Idle and rough shifting after body repair

[dphoto1]

I have a 2014 Fusion 2.0 that hit a deer when it had 3000 miles.  The deer smashed the intake to pieces and some of which went in and melted on the valves.  The head was removed, cleaned and tested for leaks.  All good.  The engine was reassembled with all new Ford parts including: intake, engine harness.   After the repair the idle would surge up and down from about 700 to 300 RPM.  It also surges when climbing a hill in 6th gear under load. The transmission will shift hard at times as if it's hunting for a gear.    It has been worked on by a Ford Master tech that was very good at drivability.   All the test confirm that it is running lean at Idle but no check engine light.   Multiple smoke tests were done with no leak found.  Swapped intake and throttle body, injectors, high pressure pump, injectors, pvc assembly, all Map sensors from known good engine.  The PCM was replaced.  As soon as you come off Idle it runs fine.  I have driven it 115,000 miles like this.  It's time to sell and would like to fix it.  Any suggestions and direction would be great.  

[mvan231]

This sounds like a possible Idle Air Control issue. Did you figure out what it was? I realize that your post was in October.

[dphoto1]

Not yet.  I have swapped the whole intake and throttle body I off of a known good car to no avail.  

[mvan231]

This seems like a very strange problem. You've swapped all the right components, but still no resolution.

 

Part of me wonders if this is something else, maybe radiator issue is somehow causing this?