Zach,
(hi - this is Heinrich from Palaeo3D)
it seems that your merging of the two components is not perfect. As a consequence, the “background deletion” algo kills part of the model, as does the misalignment along the edges.
May I recommend shooting the object not flat on a turntable, but on a pedestal (ethafoam works really well), so that you can take pictures from 0° (or even slightly below)? Then, you should be able to align all images in one chunk, without merging with CPs, which is often suboptimal.
Or shoot three or four positions: top, bottom, left, (right) down. More overlap, more chance at a one-chunk alignment that avoids the problems you have here.