You want to kit to match the case as close as possible, the gasket is the best way to do that. I you notice obvious differences with the gasket and the kit then take those into account. I would just leave the sides of the case alone since it looks like there is a little hang over on the case and the kit.
I would go alter the upper part of the case and leave the rest of it mostly alone.
Oh i forgot to mention originally that after you trace the gasket take the studs out of the case and keep the case halves together. You can access the case from any angle without the studs and you will end p with a smooth transition between halves if you leave them together. Learned that the first time, ported each half separately and when they were put back together the profiles did not match.