Been there done that with a Suz Gamma from Canada. If you MUST keep the bike, bring it in as an offroad racing only bike, strip off the street stuff before boxing it so when the customs guy looks at it he will probably believe you. (trust me, they have seen more bikes brought into the country this way than you can count). This way DOT,EPA will release it to customs and they will release it to you. You will then have a bill of sale and a "box j (or some designation) entry form from Customs. Put all the stuff back on it and go and get it registered at your local DMV with a plate and registration and title. State and feds don't talk to each other generally speaking unless the customs guy decides he wants to run the VIN to see if you were telling the truth, if he does you will get a letter telling you to re-export or crush the bike. All the above MIGHT work but probably won't so big risk here. You'll be stuck with a difficult to sell gray market bike. The only hope in hell that you have is that Ducati makes 1 bike for the world market (which includes California) that will meet DOT and EPA specs right from the factory otherwise you can get all the info in the world on what needs to be done but no one to CERTIFY that this work has in fact been done. What you need is the silver stickers that come on USA bikes because probably no matter what you do, if you don't have the paperwork they are used to seeing, you're #$%@! I sure as hell don't know everything so maybe there is a simple way, but knowing the Feds (I work for them) this will turn into a C.F. that will leave a bad taste in your mouth forever. Good Luck.
All this B.S. is why Duc NA does'nt want to help you (litigation).