Odb2 not responding to scanners no start diesel plus it only tries to turn over in neutral?

From the description it sounds like the CM either doesn't have power or it is bad. The security module is in the cluster and if it isn't registering the PCM and that the cluster is active you would get the no start condition because the lift pump wouldn't activate.
What was going on prior to this event?
As a start I would grab a test light and run all of the fuses in the boxes.

https://www.2carpros.com/articles/how-to-check-a-car-fuse
https://www.2carpros.com/articles/how-to-use-a-test-light-circuit-tester

Replace any bad fuses and try again. Also do a good inspection for any damaged wiring.

So, it did run but then quit and is a no start. I would really go over the wiring from the engine to the ECM. If you mean you have replaced the engine control module, did you program the replacement so the security system doesn't shut off the main relay?

The ECU needs to be programmed to match the truck; the engines are both the same year, yes? Dodge changed things multiple times in that time period.

So, it is turning over but it won't start, and you are not seeing fuel at the injectors? Have you tried to bleed the fuel system or is that where you say you are getting just spitting? If that is the case, then you are pulling air into the fuel system somewhere or the injector pump has a problem. You should get a steady stream of fuel.

The lift pump should prime it. To do that you turn the key on then turn it quickly to start and back to run, that should run the lift pump for about 20 seconds, repeat that a couple times and see if you get fuel from the injector pump.

So, the lift pump isn't turning on when you cycle the key? You are seeing nothing when you connect the scan tool? What year is the engine and its ECU and what part number is on the ECU? Did it come out of an automatic transmission truck? Asking because the 2003 is a unicorn, only the 2003 ECU works with the 2003 engine. 02 is different than 04. The engines are also different when it comes to the sensor outputs. I'm wondering if the issue isn't simply parts mismatch.

ECM, 5.9L (RH rear engine), California emissions, (ID 56040477AA)
ECM, 5.9L (RH rear engine), Federal emissions, ID 56028740AB
ECM, 5.9L (RH rear engine), Federal emissions, ID 56040476AB
ECM, 5.9L (diesel), (mounted to side of engine), AT
ECM, 5.9L (diesel), (mounted to side of engine), MT

Okay, what is the engine itself from? Chrysler made many changes in those years as they were changing corporate bosses. Many of their engines ended up changed in a minor way that made them not interchangeable. The most common changes were to the camshaft and crankshaft reluctor wheels. For instance, on the 3.7 they reversed the direction of the notches on the crankshaft from 1-2-3 to 3-2-1 and the cam wheels got more notches. Everything else stayed the same, the engines looked identical and would interchange fine, but they wouldn't run on the same electronics as they had changed suppliers.
I would hope they didn't do the same with the diesels, but the interchange shows that the 2002 engine is different than the 2003 and the 2004 is different again.
Looking at the individual parts isn't encouraging either, the 2003 cam and ECU only list as 2003. So what year is the bare engine you installed? What parts were moved from the original?