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You must be a wonderful person to take the time and effort to care for this child. You deserve a lot of credit. I'm sure you explained things well and with great tact and understanding. However, the fact is, that your godson needs to hear these things from an outside authority- one that is not involved personally in the situation, but maybe professionally.
He needs to hear that there is no blame attached to anyone for this turn of events. His father has an illness that causes him to do unsafe things, sometimes- no blame there- he's doing the right thing by seeking help. His mother and grandmother were rightfully concerned about his safety- no blame there, that's their job. And of course no blame should be attached to you for getting involved- it's not fair to shoot the messinger.
If anyone in the family (including the child) is getting counseling, they should ask this professional to talk to the child. Perhaps one of the program directors for the father. If this is not possible, then speak to the guidance department at the school. They should be brought into the picture, anyway, so that they can be aware of any potential problems that might impact on school. Of course, the child himself could benefit from counseling, but right now it is important to have someone who is not intimately connected with your godson, to give him this information.
The "questions and comments" he makes (particularly the ones where he seems to struggle to find someone to blame) are typical of a young child who is really secretly afraid that he himself is to blame. Children do not think or reason logically like adults. This is a jump that most would make. And its not that far-fetched in his mind, because he was there, with his father in the car. Like many children of alcoholics, whether he is aware of it or not, he feels that he must assume the "responsible person" mantle, because his father cannot.
He sounds like a really terrific kid. It's great that he seems to be coping, but if he cannot be reassured soon, he is likely to have some problems. At 6, most children will believe and trust an authority figure. Usually a caregiver suffices, but in this case all of these are mixed up in his feelings of anxiety. That is why I think someone outside the situation should talk to him. Perhaps a clergyman? Anyway, here is a list of resources for you: http://www.nacoa.org/links.htm