I am not sure on what is wrong with normals. As I do models I have my normals correct all the time.
Use p3d to check yourself (disable doubleshield in materials) before exporting and flip the wrong ones.
As for coordinates - just flip the model accordingly. There could simply be a mismatch between many different coordinate systems. If you use MS3D for exporting, the be sure to check "back to front" upon exporting.