First of all, you get up at 4:00 a.m. to wash clothes for your son to wear to school every morning???
Let that sink in a moment...
I did go back and read your previous post about your son and him having lived with his father, etc. You have a tough road ahead of you and so does your son. Many times, the best thing that can happen for a kid like yours, is to have somebody 'tough' with authority come into the picture in some way. Maybe for your son it is this bus driver.
Rather than becoming so combative over this with the driver, maybe you should try backing him up instead? Maybe he has a little more experience in the ways of how middle schoolers evade the rules than you do. Your son has only been living with you a short time, and I'm sure this bus driver has seen it ALL. If in fact, there is nothing more going on than the smoke smell, then do yourself and your son a huge favor and make some changes to eliminate that issue for you both. I'd suggest that getting up at 4:00 a.m. (cough cough) is not the best way to approach that. Washing clothes in a washing machine/dryer that is housed in a smoker's home does not get the smell out. As soon as they are dry and you take them out to fold them they are right back in a smoke filled environment, and you can smell it. Period. I had a good friend whose parents were smokers when I was a teen. My own clothes (clean, no smoking in my house or by me and my friends) came home REEKING of smoke when I'd spend any time at her house. It would even be in my own hair.
Granted, I think it is a bit extreme that the driver caused your son to miss breakfast at school. But, sometimes the schedules are tight and it can happen, even if the bus is just running 5 minutes off schedule on any given morning. But I suspect your son is 'heavily exaggerating' being held 30 MINUTES?! after arrival at school. That just sounds like a bald faced lie, to me, unless your son escalating the discussion and got sent to the principal's office for further infractions...
Maybe you should try backing up the other authority figures in your son's life, and talk to your son about how this will affect him in the longer term? Go back and read what you wrote in your first post about your son's behavior, and take that into consideration. He can't be aggressive with school officials (including the bus driver) and have no consequences. They will follow him all his life as the "troubled kid", the one with "violent tendencies", the "troublemaker" etc.... if he doesn't do something to turn it around. That is the worst thing that could happen for him now.
You mentioned getting him into counseling... have you been able to get that started? Maybe he could meet with a guidance counselor at school. He has to accept that they "system" is the one he has to work within. Being a "tough" "macho" guy or whatever he has been trying to prove will not take him anywhere good.