So, I was looking at the wiring diagram and electronic setup, as well as reading the troubleshooting literature from cummins on the engine I am buying. From the looks of things, the 5.9 CR and 3.9 CRs are wired nearly identical except that the pin outs from the primary ECM connection are reduced for the 4 cylinder. Then, looking at this literature on the function of the dual CP3 programmer, the CP3 pump manages the injection pressure at the rail based on the ECM input, if this controller I linked to below goes between the pump signal and modifys it prior to the injectors, then its possible that it may work just fine with the 4 cyl, or could easily be modified by the manufacturer to work with the 4 cyl. Then again I could be WAY wrong. It is however, a thought to consider. I went ahead and emailed them this morning to see what their thoughts are on the matter. I will report back with what I find. They claim 20% gains with adjustability on the fly. I would love to have something like that snuck under the dash of my project.
http://www.tsperformance.com/Download/pdf_Files/Misc. Instructions/Dual_CP3_Instructions.pdf
http://www.tsperformance.com/Download/pdf_Files/Misc. Instructions/Dual_CP3_Instructions.pdf