One thing that I can think of having done a few engine swaps is that the tone wheel (aka reluctor wheel, trigger wheel, etc.) that the crank sensor is sensing may have a different tooth configuration. The teeth and gaps on these wheels is what creates the square wave output used by the PCM. The cranks sensor usually is only used to indicate that cylinder number 1 is at TDC or some degree from TDC. The crank signal is also often the only sensor required for starting the engine. The cam sensor is used for acurate fueling and spark advance. The expected crank and cam signals are used to determine misfires as well, so you really need the correct PCM matched with the correct Cranksensor location, and the correct tone wheel.

The configuration of the tone wheel can vary by tooth count, tooth width, window width, or intentional gaps left in the wheel.

This is an interesting post that might be related: https://dodgeforum.com/forum/1st-gen...ml#post1443995