Idisagree,
The first thing to say is that your son has not been excluded. A half day in an internal exclusion facility is not a formal exclusion and whilst I have no doubt it will be on your son's school record it is not an exclusion.
If you look at the guidance for formal exclusions then for an exclusion of upto 5 days the headteacher does not need to inform the Governing Body about the exclusion immediately only once a term in a formal report. However the GB must in such a case consider any representations made by the parents. However they cannot re-instate and can only place a copy of their findings on the pupil's school record. But your son has not been excluded formally.
Appeals to an independant appeal panel can only go forward in the case of a permanent exclusion.
The reality is that you have no case for appealing the half day internal exclusion. What you do have is a complaint about two aspects of the situation. Firstly the fact that the school is not taking your son's statement seriously and secondly about the manner in which the school acted over this minor incident.
As far as SEN statement is concerned, I would suggest that if you do not get a cast iron guarantee of the school implementing what is in the statement that you go to the LA and ask them to investigate. They will be less than happy if they are putting funds into the school which the school is not using correctly.
From your description it would appear obvious that the school have handled the incident badly and to change their mind three times on the punishment is just ludicrous, it makes them look fools. They did not carry out a proper investigation before coming to a decision about it and part of that investigation should have been the school allowing your son the opportunity to put their side of the story.
I am not sure that you can expect the GB to do anything but, if you have made a formal complaint, to accept that the school got it wrong and that they will do better next time. Given that the final punishment was half a day in internal exclusion I would not expect the GB to do anything about that, no matter how innocent your son was and I don't think from what has been said in your posts that he was entirely innocent, he did do something albeit probably under a level of stress / presure.