i do not think a silencer has anything to do with it... I too live in the bay area...
What kind of car do you have and what gen b16 is your motor???
I just helped one of my buddies 90 civic DX hatch to pass with a B16sir2, and an OBD1 conversion...
What we did to pass...
first time:
we went to the ref place at skyline collage...
opened the hood of the car, and the ref said that the motor better be obd2 or say B16a3 on it of he will not even look at it. We then turned around and left.
Second time:
took it to Fremont at like a sequoia institute ref station
told the ref it was from a del sol VTEC
he wanted to see the cat and make sure it was atleast up to DelSol VTEC specifications, by luck it was...
My buddy also had his stock civic muffler put back on too...
He passed, without any other problems.
if you have questions e-mail PM or IM them to me...