In order to advance the current research engine to operate in advanced combustion modes such as reactivity controlled compression ignition RCCI a diesel common rail fuel injection system for the experimental research engine has been designed and developed through testing the hydraulic, electrical and electronics, mechanical subcomponents, and the controls strategies. This study presents the process taken based on the verification and validation model of design and development for the fuel injection system incorporating hardware-in-the-loop (HIL) testing prior to engine operation and subsequent engine validation. 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 PI 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°, 15°, and 22° 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 when comparing single pulse common rail events. 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° and 22° BTDC. The AHRR displayed cool flames at 24° BTDC along with a reduced peak at 35 J/CAD and prolonged diffusion burn. These are preliminary results on a continually growing research engine. A port fuel injector (PFI) is also introduced into the intake manifold to conduct tests in RCCI mode with alternative fuels such as various Fischer Tropsch fuels and n-butanol. The spray pattern of the new piezoelectric injector was modeled to investigate the relation with excessive soot production. The results show 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, and for these reasons a custom injector is being designed to resolve this issue. 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.