*Clears throat* You didn't answer Annatar's question.
Best thing I can suggest, and to any new modder, is to change one thing, load and test. If successful; add another. If it fails; tweak and adjust and/or ask on the forum. You have changed a lot, and to just 'hope' it will work first time was very naive of you.
I have done the Capital ship -> Frigate conversion you speak of, and had no problems. I use 'Compare It!' which is a free file comparer and merger, I strongly recommend that. Then you can see exactly what is different in the 2 file types.