Can the 5.9 computers be programmed to run a 4 cylinder engine?

I have an ISB170 3.9 which uses the same injectors, rail pressure sensor, fca, etc. as the dodge/cummins 5.9. However it uses and industrial (J1939) protocol which no one programs. If I re-pinned the harness to connect to the dodge/cummins computer does the EFIlive have the capability to time the 4 cylinders appropriately? I know the industrial 3.9 and 5.9 use the same computer just different programs.