Firstly, could I please ask you to stick to one thread for posts about your case? It helps us to keep track of the full picture, and is effectively your own "11+ Q&A section". Thank you! Just for my own reference - and for others if they wish to follow the case - the original thread is here:
You can certainly apply for a manual re-mark. Simply email Admissions and they will advise you how to proceed from there. There may be a slight delay in replying because this week is incredibly hectic for them.
If your son's marks were in the box, but extended beyond it, the computer will still have picked them up. It is only if they were not in the box at all that there is a problem.
I have to warn you not to put too much store by the result of the re-mark though - the computer has proved to be very accurate since it was introduced.