Regarding the missing parts please try some of this recommendations:
- Always use a reconstruction region.
- Change the RECONSTRUCTION REGION slightly, say +10-15 % bigger and rotate it by say 10-15 degrees.
- Set Minimal distance between two vertices (Reconstruction settings - Mesh calculation) to some value, e.g. 0.001
- Raise the number of Maximal vertex count per part (Reconstruction settings - Advanced) to higher value, e.g. 10M or 20M