Migration Tool creates a virtual FSX installation, meaning that it will turn an empty folder of your choice into looking like the FSX root folder, with all necessary configuration files present. Everything installed there - no matter if by hand or using installers - will appear in Prepar3D.
The tool works with almost every FSX addon out there.
However, there is something upsetting FDC, thus producing the fault message mentioned.
If we knew the cause of the message that would perhaps be of some help.
In my opinion, it is essential that FDC works with P3D because, slowly but surely FSX is on the decline.
If PFE works with P3D why not FDC
Regards Eisbahn