You also have a limited pallet of subVI/primitives to choose from when you are working with embedded. Many of the file IO VIs, for example are not available on an embedded platform so they are not available for development. I don't think that they would be correctly converted to C-code.
If you limit yourself to the VIs available in the embedded package, it should work. And yes, $11,000 is quite a step.

All in all, I think that you would be better off calling LabVIEW built .DLLs
Good luck,
Bob Young