After many more hours scanning I have found a really good alignment tool is a small block of wood, wrapped mostly and randomly in black vinyl electrical tape. This keeps the captured scanned data small from the block, but the grains of the wood are random and the scanner does pick them up so the alignment is virtually exact each time. Another benefit of the wood is the grain is a very subtle surface deviation that can be picked up with a very small included angle from the surface of the block. This way when you take a scan from the opposite side of the block, it will still pickup the same grains it did before. By contrast, spheres and any other objects that are more pronounced (unless the software is designed to derive an alignment center-point from the sphere - like high end metrology scanning software programs do) will not align if you take another scan from 180 degrees of the previous scan... there just are no points that overlap. The near flat textured wood surface is an excellent alternative, at least until the software has sphere alignment in it.

Regards,

Dave @ Nerv