My oldest ds had a lot of trouble with transitions. He has AS and I guess this is common to kids on the spectrum. Your daily struggles sound very familiar. We found that preparation and routine really helped a lot. We made sure that DS had his clothing all the way to socks laid out the night before. We had to go over a specific routine with him, or he'd wander about half dressed and not sure of it was time to eat breakfast or time to brush his teeth. Once he had a schedule (and I put estimated time onto it to keep him on track) he was fine. Otherwise, every morning was new and different and something he passively or actively resisted.
I have to politely disagree about sending him to school in jammies. That is just asking for teasing and ridicule. Don't go for public embarrassment; try to support his organizational and motivational challenges.
