Andy my friend your motorized dish sander looks pretty slick - very nice job!
1) I can't remember if the Stew-Mac kits have pre-profiled sides or not. In any event, even if they do I doubt that they took the radius directly from a dish with a method like Colin's that uses the actual dish to transfer the profile to the sides. What radius is your dish? Anyway the gap that you see is not unusual to have when the sides have simply been cut and not pre-profiled. Also you know to sand the radius in prior to installing the kerfed linings right and then glue in the linings slightly proud 1/16th - 1/32nd" and hit it in your motorized dish sander again.
2) I am not real sure how well the Stew-mac cheap-arse waist clamp will hold up while using the motorized sander. Most people use a mold that supports the entire rim so be careful. In fact since you don't have an outside mold it might be a good idea to glue in the linings when you are getting close to rim contact all around. The linings will provide some additional support to the rim and help it keep it's shape. Nothing special is needed to keep the neck block lined up because the irregularities in the dish will be spread out, since it is spinning to the entire rim. For manual dish sanding, what Neanderthals like me do.....

I flip the rim and mold 180 degrees every so often when I need to hit the dish with the shop vac to keep the dust from clogging the paper.
3) Your neck should be fine but the guitar's neck will need to be fitted which is part of building. Do you have a dovetail or bolt on? In either event some fitting is required once the neck block has the radius sanded into it.
BTW that sanding stick thing actually works pretty good although a dish is way better. One of the great things about Stew-mac kits is that you don't have to have an outside mold or sanding dishes.
Looking great Andy!