Neutron scattering studies on a c-axis polarized B 2 u phonon and magnetic excitations of the YBa 2 Cu 3 - x Zn x O 6 + y system were carried out. For YBa 2 Cu 2 . 9 Zn 0 . 1 O 6 . 7 5 , anomalies of the B 2 u mode related to the spin (pseudo) gap formation are insensitive to the Zn-doping. In the magnetic excitation spectra of YBa 2 Cu 3 O 6 + y samples which are close to the metal-insulator phase boundary, a gap-like structure can be seen at high temperatures, while at low temperatures the low energy spectral weights increase and the gap-like structure disappears. This suggests that the itinerant nature has an important role in the spin gap formation.