A diesel common rail fuel injection system for an experimental research engine has been designed and developed through testing the hydraulic, electrical, mechanical subcomponents, and the controls strategies. This study presents the process taken based on the verification and validation model of design and development for a fuel injection system incorporating hardware-in-the-loop (HIL) testing prior to engine operation and engine testing. Software verification was completed through signal converting circuits to confirm precise injection timing and to test the system in a mean effective model to incorporate a PID speed controller along with consistent rail pressure. Initial operation of the common rail system integrated on the direct injected single-cylinder medium duty engine resulted in flexible combustion schemes with various injection timings and split patterns at a constant speed of 1500 RPM and 4.2 IMEP. Swept injection timing was tested from single pulses at 8°and 15° before top dead center (BTDC) to multiple pulses starting at 60° BTDC. The original injection was at 15° BTDC and by delaying the timing to 8° BTDC, in-cylinder pressure reduced from 71 bar to 53 bar and the AHRR (apparent heat release rate) peaks decreased from 160 J/CAD to 70 J/CAD. These changes reduced NOx emissions by 98% but in turn dramatically increased soot and unburned hydrocarbons by over 10 times. Multi-pulse injection was also tested with 30% of mass injected at 60° BTDC and 70% at 8° BTDC. The AHRR displayed cool flames at 24° BTDC along with an reduced peak at 40 J/CAD and prolonged diffusion burn. The spray pattern of the new piezoelectric injector was modeled to investigate the relation with excessive soot production. The results showed that the new spray pattern impinges on the cylinder head with high levels of wall wetting and film formation resulting in a slow oxidation process with increased unburned hydrocarbons. The new injection system and associated controls implementation of this system allows a flexible injection scheme and combustion phasing control nevertheless, the calibration is continuing including harmonization with the EGR and supercharger systems.