I am unclear as to whether we should set out our case for a place at this school against the GS school we have been offered, or in comparison to the middle school he attends now, as he could theoretically stay at until the end of year 8.
Neither! You're not appealing against your second preference or against the middle school - you're appealing for your first preference, so that's what you should try and focus on.
Whilst I am a little more clear of what type of thing we should include in the presentation on the day, with regard to the information we submit in advance, should this just be centred around evidence (of predicted SATS/teacher assessed levels etc) or should there be things in there such as our reasons for wanting him to attend this school (like his sibling goes there, logistics of getting children to school etc..)
If he's qualified, then you don't need to provide evidence of grammar school ability. It would be superfluous.
However, if by chance places were allocated in rank order of score, then you might possibly wish to put forward a case that he was expected to score even more highly than he did, and to provide supporting evidence.
Otherwise, you should just concentrate on your reasons for wanting a place.http://www.elevenplusexams.co.uk/appeal ... -school#c2