Realise this is an obvious one but what's worked for me - and is method currently using for SP Game Update - is rather than link to new models, have simply
replaced the stock models with new ones. Avoids messing around with any scripts or PY files

So for example, just delete the current Galaxy nif and textures, and copy/paste DJ Galaxy nif and textures to the empty Galaxy folder. Then rename DJGalaxy nif to Galaxy nif. Voila

Most hardpoints I think have left as original as scalings usually ok, but again easy enough to change or update. Using this method also avoids any ship name errors in Maelstrom scripts.