No, the CHP is to issue the VIN#, sounds like the clerk didn't know how to handle an SB100 (most don't as it is an unusual procedure)
You really needed to be doing this weeks/months ago, you might be boned as the time it takes to straighten out your paperwork will be time lost for the DMV to call into Sacramento for your sequence number, when I did mine all the numbers were gone by 10am.
That said, I heard that they didn't sell out the sequence numbers this year, so you may still have a chance, apparently the economy slowed people down.
I highly recommend the the Thousand Oaks DMV, they have a lot of experience with the process but word has got out about them, so get there really early.
I started my process months in advance and and even with the TO DMV's experience the first clerk I had didn't know about it and messed it up (and I didn't catch it), so I had to go back a second time and got the manager to sort it out. I then went back a couple of weeks before just to have them double check my paperwork and they still found some mistakes.
Good luck