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Proton radiation therapy is a fast growing form of cancer treatment; it requires a precise knowledge of the dose delivered to the tumor and verification of the correct patient position with respect to the proton beam to avoid damage to critical normal tissues and geographical tumor misses. In existing proton treatment centers dose calculations are performed based on conventional x-ray computed tomography (CT). The goal of the Proton Computed Tomography (pCT) project is provide a fully operational detecting system that allows imaging of the patient (or a phantom) directly with proton CT by measuring the energy loss and trajectories of high-energy protons that traverse the patient. The pCT detector contains the upstream tracking detectors, phantom, the downstream tracking detectors, and a calorimeter. The step-by-step assembly of the pCT NIU Phase 2 Scanner and the subsequent tests and calibration procedures are described in the current work.