Unfortunately NFX 2 and SP are not compatible. If you want to play the campaign you have to have basically a clean install. Foundation is Ok, as are additional ships, but thats about it.
Also when you install replacements for the stock Bird of Prey, Keldon, Warbird, Sovereign, Nebula, and Akira, you have to make sure you edit the RanKuf.py, MatanKeldon.py, E2M0Warbird.py, Enterprise.py, Peregrine.py, and Geronimo.py in the scripts/ships folder to make sure they all use the correct models or else you'll get crashes.