I downloaded the patch in his first post - 1.3. The first patch, for me, actually deleted the Next War units in both the city build and Worldbuilder.
I definitely have replaced the last Expanded file.
It looks to me, as I went in and played around with the World Builder and city for a while, that the SDI is no longer considered a wonder but a Spaceship thing. It's definitely there, though not in World Builder (Manhatten Project's not there, either), but you need Space Victory on and I don't use that victory. Apostolic Palace wasn't on the World Builder, in the city building mode, or in the Civpedia.
By the way, I think someone said there would be more powerful ships in Next War, but I haven just got 40 strength Missile Cruisers and Battleships, etc, still.
I'm playing the mod on earth, Warlords or original map, 18 civs.