I installed and setup the v2 migration tool and none of the CS stuff shows up.  

So, I tried your "just copy the files" --- Captain Sim dir off the main FSX dir and all the aircraft folders.  But when I load the base 757-200, I just get a black / blank VC.  The 777 loads, but eventually something causes P3D2 to crash.

The only thing that seems to show up with the tool are  the FSX default aircraft.