Sorry, but more info has come to mind.
It's the Department of Motor Vehicles, not the Department of Motorcycle parts. You can't register a "box" of parts, nor can you register a frame or motor. You must present a (more or less) complete "vehicle" to register it. It doesn't need to run, nor does it matter if the electrics work, etc. A title shows a registered owner and is nearly useless if it hasn't been registered for over 7 years. The "Bill of Sale" is more important to the DMV so that they'll know how much sales tax to charge you.
You can register anything without a title in Ca., if you do a VIN Verification first. In your case, where you're building a bike from parts, you should take the motor and frame and trans too if it has different #'s than the motor and have them checked at the CHP to see if they are stolen. If they are clean you should get some paperwork for it. Then build your bike. Go to the CHP again with a bill of sale for the frame, motor, and trans. If you don't have any, fake it. You bought these parts at a swap-meet. All of the other parts were bought new at a Ca. retailer, so you have already paid Ca. sales tax on those items, so you should only have to pay taxes on the purchase price of the motor, frame and trans. Bring a handful of receipts to document this. Again, do this at the CHP. When you're finished there, then you go to the DMV, and the only paperwork you need to show them is the VIn verification form from the CHP. It will have the purchase price of the vehicle on it.
Easy!