Hello archaeological_pt,
I think you should take several circles of images from different heights, also you'll need to roll the object over to take pictures of the bottom from out side.
Processing both subsets in a single chunk will require masking out the background prior to processing.
As for the inner part, it will be included in the result if you have good quality images that contain both outer surface of the object and inner parts (opposite sides). Both these surfaces should not be blurred, so you'll need to use higher F-stop values.