The Kyoto Tridimensional Spectrograph II (Kyoto 3DII) is an optical integral field spectrograph mounted on the Subaru telescope as a PI-type instrument. Used with AO188, Kyoto 3DII provides us unique opportunities of optical Integral Field Spectroscopy (IFS) with adaptive optics (AO). While AO works better in redder wavelength regions, quantum efficiency of the previous CCD was low there with optimization for a wider wavelength coverage. To optimize Kyoto 3DII to AO observations, we have newly installed the red-sensitive Hamamatsu fully depleted CCD, which enhances the system efficiency by a factor of ~2 in the red wavelength range. Fringes are dramatically reduced, and the readout noise drops to 3:2-3:4e- about two times smaller than previous, due to refrigerator and readout system. With these improvements, we carried out engineering and scientific observations in September 2015, February and March 2016. We measured the system efficiency using a standard star, and confirmed the successful improvement of the system efficiency. We observed galactic nuclei of nearby galaxies in the Natural Guide Star (NGS) and the Laser Guide Star (LGS) modes. We found the spatial resolution of ~0.1′′ FWHM using a 9.5-magnitude NGS, and ~0.2 - 0:4′′ in LGS mode. Together with the AO resolution, improved efficiency opens a new window for Kyoto 3DII to carry out high resolution optical IFS targeting faint objects such as high-redshift galaxies as well as faint lines such as [OI] λ6300° A and absorption lines of nearby objects.