Welcome Jeff!
You have to jump through a few hoops to register your car under SB100, but don't lose any sleep over it. The process is fairly standardized and there's a ton of resources and well documented threads on Club Cobra that walk you through the process.
This year, the 500 SB100 sequence numbers were not all issued on January 2nd. As of a couple of weeks ago, a number (35+) of SB100 sequence numbers were still available.
Once you get your car and have an MSO from the manufacturer, you can apply for an SB100 sequence number (provided they are available). Your car doesn't have to be completed and all you have to do is estimate the cost of the engine and transmission.
You can ignore everything you've heard about registering or passing smog against the year of the block. All new SPCN (Special Construction Vehicles) in CA are registered under SB100. You can build the engine exactly how you want it and it will be smog exempt for life under SB100.
Good luck on your build.
P.S. Here's an excellent thread regarding SB100. Also, use the search function and soak it all in.
SB100 newbie question