Honestly I think you are better off with a regular head unit and an ipod, not sure why you want the apple... You are going to spend all that money on that system when a simple cd player and nice set of components will sound better... and be less trouble, I don't know of a toslink cable that is going to like being bounced around and constantly moving, I have had them go bad just lying behind the audio rack untouched...
Anyway I think you are better off asking this question on a car audio forum, them guys most likely will know better what to use for cables in a car.
I know people have used mac minis in cars before, I seen pics of a system not long ago, but for sq I don't think its going to be any better than a decent head unit..