If they bolted up they are compatible isn as ense. The isssue ifs witht the sensors, injectors, injector drivers and the ECU. You may be able to switch some over but more than likely you will neeed to take apart the wiriing harness from both trucks and make one engine harness out of them both that works with one of the ECUs. You could decide by which one makes the best power or will be the least amoutn of work to do. You will neeed and ECU pinout for each and we do not have those really. You would have to extraplotate them from the wiring hranesses.
You might look around the internet for someone who specializes in swaps like this one.