johnnyp,
my .02 cents; I'm with BudBandit - it's the road.
my commute is from the far East Bay down to San Jose, and there are stretches of 680 (especially heading south about a mile or so before the merge with 84) and down around Milpitas or thereabouts) that are simply HEINOUS! The rest of the time it's pretty decent. When I commuted in and around the city, I don't remember having that much trouble.
And I ride a Blackbird, a bike that is usually pretty smooth and has a longer wheelbase than most sportbikes.
Makes you wonder what they're thinking when they make these roads. Come on, we're in the 21st century, can we not make a SMOOTH roadway.