My advice is to not let the close calls shake you, and accept them as part of riding a motorcycle. I can say that I've had just as many close one's in the car as on the bike because of stupid people on cell phones, etc. I almost wrecked my GS500 on the way to trade it on my M50 because a lady ran a stop sign at a "Y" in the road, and even with my laying on the horn and looking down at her front bumper, she still kept coming. Luckily the 500 had enough zip to get ahead of her, but if I was in a car I would not have been able to avoid it at all.
My theory is that once you accept that there will be close calls, you get more alert to them and consious of them. I look at close calls as a way to keep you on your toes. I'm also a private pilot, and had a few close calls on landings, but look at those as the best learning experiences I've ever had. Nothing like facing death to stick a lesson in your head. I bet everytime you go out you remember what you did wrong in fixating on that car and are very aware not to do it again. Count it as a blessing in disguise.
oh - maybe this is coming from my tag line below from Theodore Roosevelt!