I would suggest first reproducing the band structure as in the tutorial to see that you have the right structure and band gap. Regarding DOS, it is not clear what you are actually showing in that picture. Also, why do you think there is no contribution of d-orbitals, e.g., to some of the states that are far from the Fermi energy?
Regarding IV calculations for a perfect ballistic system with the ballistic leads made of the same material as that of the central ("scattering") region, the only quantity that makes sense in this case is the Transmission Spectrum and related ballistic conductance of a perfect crystal at V_dd=0. So, I would calculate the transmission spectrum at V_dd=0 to see if the gap in the transmission is consistent with that in the band structure. Note that you should use sufficient number of k-points to converge the transmission spectrum, i.e., you have to increase the k-point grid density until reaching the convergence.