Neil,
It wouldn't really make any difference if the owner of the car registered the car as a 1965. When you bring a car that was previously registered in another State, the State of CA first wants to know whether the car was legally titled in that State that you're purchasing the car in. In NV, I believe that a 2003 title would be appropriate.
So, you should be able to walk in to a DMV office with the existing registration and tell them that you want to register the car as a SPCN and plan to go through the SB100 process.
Here's the latest and greatest thread regarding SB100
SB100 Conference at the MUSTANG RANCH
It's my understanding that (in most cases) people who have brought a previously registered car into CA don't need to worry about the MSO.
BTW - I chose body style per the recommendation that others had provided. They will ask you at the BAR what "design year" the engine is from. Here's the excerpt from the directions that Steve documented in the SB100 link above:
• "They will review your car with you and make sure you let them know that the engine is from “design year” 196x (whatever your year.) as they will go look up the year and displacement and notate what is supposed to be there PCV, etc. ( I personally recommend use of 1965 ford 7L. for a 427 and a 1964 Ford 4.7L (289) for small block."