I just went through this with an old old old out of the system bike. Here's what you do:
1) go to the DMV and try to register it as normal (you should be able to get a clean title, just don't dwell on where you bought it from)
2) they will put it through the system, and then give you your paperwork immediately
3) in about two weeks, you will receive a statement in the mail that you need a CHP inspection to complete the registration
4) set up your CHP inspection (if it will be a ways out, then go get a temporary operating permit from the DMV so you can ride in the meantime)
5) got the CHP inspection (only ride the bike if you have an M class endorsement and the temp operating permit, otherwise trailer it in there... or they will tow it and ticket you exorbitantly)
The CHP inspection is a formality. Even if you went in there with a rotten piece of garbage with mismatching everything and smelled of weed, barf, poontang, beer, and cigarettes, they still wouldn't take more than ten seconds inspecting your motorcycle. In other words... don't worry about it.
HOWEVER!!!!!! #@$%@#$@#$@#!!!!!!!111!!!!1one!!!!111!!! MAKE PHOTOCOPIES OF YOUR PAPERWORK!!!!!!11!!11111!!11!ONE!! The Sacramento DMV office is great at losing specific pieces of paper that you send in (not all, just one or two). Thank God I wasn't pulled over any time in the last few months, because my bike was apparently never fully registered. If I had been pulled over, then i would have given up the bike because the "no registration" fees would have been excessive. So, another point to bear in mind is that you really need to follow up to make sure your registration has been completed. If not, then you will receive another letter in a few months stating that you better finish up the process.
Good luck,
Camelman
PM me if you have any other questions.