If you are referring to Lindsay Porter's mini restoration manual, it is not worth the paper it is printed on. He missed quite a few important points. You will learn far, far more on this forum. I strongly recommend reading right through some of the restoration threads. You will see some very ingenious repairs that are not in the book.
If the engine is out, there is less stress on the shell, so less chance of distortion when you cut bits out. But I would suggest keeping the subframe in, and if you are going to fit a solid subframe mount kit, do it now, rather than later, as it will help to keep the front correctly aligned.