I think it is pretty obvious that he treated the Phase II E as a true refit.
One of the clues is how closely the interior section view from TMOST matches the interior section of his Phase II ship. Even the turbo paths match. It has also made me wonder if there wasn't a large, detailed section view of the original ship in his possession when he drew the new one. I mean, he even plotted out the deck thicknesses and locations of various rooms. Is there still a TOS Jefferies cross section kicking around out there somewhere? What I wouldn't give for a look at that!
As for Maurice's question: I don't think a complete high resolution scan of the Phase II drawings have ever been released to the public.