If the vertex IDs are correct, and it's just the winding order that is an issue, you could:
- Take the face model that you get as part of the Face Trainer download package
- Add your modified face mesh as a blendShape target
- BlendShape the model and then delete history.
If the vertex order is also different, you could try using the TransferAttributes tool in Maya, using UVs as your correspondence and vertex position are the attribute that you are copying.
Otherwise, you might be best off using a tool like Wrap3D to register our face topology to your face model.