First of all, you are right on target with many of the approaches you are using.  Taking time off from work for this milestone in your son's life (his first day of school) sends a valuable message, that school is very important.  The communication with the teacher through the notebook as well as conversation is going to help your son know that you are supportive of school and the expectations they have of him.  Using stickers and rewards are great for encouraging positive behaviors.
The problem you are dealing with however is decreasing the negative behaviors.  There are some techniques that are very effective in decreasing those behaviors we don't like.  Specifically the problem with story time can be affected by setting expectations, teaching a skill and practicing it at home.  The skill is Listening and can be taught in steps to your son.  Because of his age and developmental level, keep it simple.  The skill has just 3 simple steps, 1.) Look at the person.  2.) Sit or stand quietly.  3.) Say "Okay."  After you teach this skill to him, then practice it by reading him a book at home expecting to see these steps during the reading.  If he does not meet your expectations by looking at you, sitting quietly, and saying "Okay", stop reading, describe what he is doing wrong, give a negative consequence, re-teach your expectations and have him practice by resuming the story.
Consequences have to help him understand the contrast between what happens when he behaves and what happens as a result of misbehaving.  Remember that negative consequences can be loss of priviledge or addition of a chore.  Use the smallest consequence that is effective.
Pick your battles and work on one skill at a time.  Since the current issue is Listening, start there.  Good luck and remember that you are your child's first and most important teacher.
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