I got it to work, Thank you Zebra 9.
For everyone else I'll tell you how I did it. It's kinda more complex than it looks (or should be)
You need a mod with the following files
GameInfo
CIV4ProjectInfo.xml
Buildings
CIV4BuildingClassInfos.xml
CIV4BuildingInfos.xml
Units
CIV4UnitInfos.xml
Terrain
CIV4BonusInfos.xml
Text
CIV4GameText_Civilopedia_Bonuses.xml
CIV4GameTextInfos_Objects.xml
In CIV4ProjectInfo.xml you need to erase the Manhattan Project and set the required project for the SDI to NONE.
In CIV4BuildingClassInfos.xml you need to create a building class BUILDINGCLASS_MANHATTAN_PROJECT with no world limit, no team limit, 1 per player, and no extras.
In CIV4BuildingInfos.xml you need to set the Bomb Shelter's specialbuildingclass to NONE, and create a building of building class BUILDINGCLASS_MANHATTAN_PROJECT. The Pentagon is a decent template. The building should cost 1500, allow nukes, get a production bonus from Uranium, cause no great person points to rack up, cause no happiness or sadness, or sickness, or health, ect. Like the project would do. I used the art for the bomb shelter as the art. It should also give the civilization that built it 1 resource called "Weapons grade"
In CIV4UnitInfos.xml I changed the tactical nuke as well as the ICBM to require weapons grade as well as uranium.
In CIV4BonusInfos.xml I created a resource called weapons grade that can be found nowhere on the map (hit movies is a good template), I used the uranium art.
In CIV4GameText_Civilopedia_Bonuses.xml I described weapons grade uranium
In CIV4GameTextInfos_Objects.xml I created a key so that weapons grade uranium won't be known as hit movies.
That all should work, plus the United Nations will ban Manhattan Projects if nukes are banned. I would upload the mod, except I have one question. Will the AI figure out what it has to do to get nuclear weapons?