Procedures and results on hardware-level detector calibration in Super-Kamiokande (SK) are presented in this paper. In particular, we report improvements made in our calibration methods for the experimental phase IV in which new readout electronics have been operating since 2008. The topics are separated into two parts. The first part describes the determination of constants needed to interpret the digitized output of our electronics so that we can obtain physical numbers such as photon counts and their arrival times for each photomultiplier tube (PMT). In this context, we developed an in situ procedure to determine high-voltage settings for PMTs in large detectors like SK, as well as a new method for measuring PMT quantum efficiency and gain in such a detector. The second part describes modeling of the detector in Monte Carlo simulations, including, in particular, the optical properties of the water target and their variability over time. Detailed studies on water quality are also presented. As a result of this work, we have achieved a precision sufficient for physics analyses over a wide energy range (from a few MeV to above 1TeV). For example, charge determination was at the level of 1%, and the timing resolution was 2.1ns at the one-photoelectron charge level and 0.5ns at the 100-photoelectron charge level.