The Cornell Energy Recovery Linac (ERL) prototype photoinjector was built at Cornell University several years ago. The goal was to demonstrate that the photoinjector can produce the ultra-low emittance and high-current electron beam that will be used for the entire Cornell ERL facility. A high repetition-rate highpower Yb-doped fiber laser system produces the electron beam from a photocathode. The photocathode is one critical component of the photoinjector that can produce electron beams with low emittance, short bunch length, and high current. On the photocathode, the laser pulse shape maps to the electron bunch profile, and this mapping becomes complicated at higher bunch charge because of the virtual charge effect. The uniform ellipsoidal electron bunch distribution is the optimal distribution, because the linear space charge effect can be compensated by the linear optics downstream; the optimized laser pulse shape can be different because of the complicated mapping from the virtual charge effect. In order to achieve the optimized laser pulse shape, it requires threedimensional (3D) laser pulse intensity shaping and 3D laser intensity diagnostics. We demonstrate the fidelity and accuracy of the 3D laser intensity diagnostic from a noncollinear first-order cross-correlator, and the optical temporal phase retrieval from the same setup. We also present the slice emittance measurement, that is, the time-resolved emittance measurement, at both near-zero charge and 77 pC; it provides insight into the emittance compensation process and contributes to the emittance optimization. The calibrations and related issues are discussed as well. With such capabilities, we achieved the smallest emittances that have ever been measured from this photoinjector at 5 MeV beam energy with usable bunch charge, which was reported as one milestone of the Cornell ERL.