Registration and SB100 are really two separate things. Your first issue is if California will recognize the title from New York.
From the DMV:
" Anyone who brings a vehicle into California, or purchases a nonresident vehicle while in California, should be aware that some nonresident vehicles cannot be registered in California or the United States (U.S.). For rules and exceptions, see the Buying a Vehicle From Out of State-Can You Register It in California? (FFVR 29) Fast Facts brochure on the Department of Motor Vehicles (DMV) website at Detail
Caution: Unless the vehicle was originally manufactured to meet California emission standards or the owner or vehicle qualifies for an exemption, California law prohibits:
California residents or businesses from bringing into California or registering in California, a motor vehicle that had less than 7,500 miles on the odometer (at the time of purchase, trade, or acquisition).
Anyone from importing a new direct import vehicle less than two years old."
Once you get past the issues regarding out-of-state registration, the SB100 will be no issue at all. You will be able to get the SB100 for the 1969 351 without doing anything to the engine except perhaps a PCV valve, which is no big deal.