I'm not sure I follow what you're trying to do... Are you wanting to put the diesel engine and front axle onto the jerk-a-matic or do you want to put the diesel engine into the RC chassis?
Basically... I believe if you want to maintain the RC platform and steering then you need to use the RC front axle, bolster and sheet metal... so just swap the engine and flywheel... AND GET A DIESEL RING GEAR for the flywheel.
Otherwise... if you want to use the AP front axle and bolster you'll need to change the back end over to a straddle mount and take the steering with it. I don't believe the sheet metal will interchange fully between the RC and AP models.
Why you'd want anything to do with this swap is a bigger puzzle to me...