Hey colleen,

Very sorry to hear about your friend. Keep us updated an how he is doing. I am struggling with the same thoughts and fears.

Here's my list:

1. Ride very defensively. You know the common problems, e.g. passing (standing) vehicles from the right, intersections, dooring (reduce speed if the 3+ feet is not doable), avoid making your commute about excerise if you need to ride in city traffic (you're in San Francisco, I assume) - it takes too much focus from traffic to the speed, heart rate you want to maintain. But don't ride scared!!! (I see these people that will hug the curb, shaken by every car that passes them).
2. Wherever possible try to find the route with low traffic volume and low-speed traffic. If I had to commute on 40mph roads, I wouldn't do it by bike. I go out of my way to find segregated biking facilities or residential roads in order to minimize chances of getting hit and lower the probability of severe injuries.

Ride in a way that makes you comfortable. It's no fun, if you're scared.