1. please refer to the discussion in the following thread:
http://quantumwise.com/forum/index.php?topic=2026.02. the reasons for your results different from those reported in literature could be quite complicated, e.g., even the thickness of nanowires are the same as those in literature, the atomic positions and the computational setup (e.g., some key parameters in the computational method) may be different. To reproduce the results in literature, it usually needs more patients and carefulness. Sometimes it is necessary to contact the authors of the original sources in order to figure out the exact reasons, because more or less details of computational setup were hidden in paper.
3. As said last several posts, you cannot apply biaxial strain to an individual nanowire. The manner illustrated in your image is not applicable because the lattice constant A includes the vacuum thickness. The change in the lattice constant A is just to alter the vacuum thickness.
4. Yes, the effective mass of a nanowire can obtained by following that tutorial.