No migration tool. Used the new installer from the FSDT site. Where are the vehicle files located?
If you use the installer, it will install them in the proper location. And, you should have seen some error if vehicles were missing so no, they are not probably missing.
Try to reset your graphic settings, by removing the Prepar3d.cfg file in the %APPDATA%\Lockheed Martin\Prepar3d v2 folder, perhaps you applied a tweak that shouldn't be applied in P3D.
It might also be a problem with the P3D shader cache. Try to rebuild it by removing the following folder:
%LOCALAPPDATA%\Lockheed Martin\Prepar3d v2\Shaders
And then start P3D. On the first launch, it will take a while for the scenery to appear, because the sim is rebuilding its shaders so, just wait and it should come up eventually.