New ECM, gauges not working, engine running rough?

Hello, what was the reason for replacing the PCM? If you components that are not functioning correctly now, and the only thing you did was replace the computer, then there are two possibilities, either you received a bad reman PCM (which happens all the time), or when moving around the PCM connectors, the pins inside the connectors are not making good contact now. This happens on these older vehicles, I just dealt with this yesterday. Look inside the connectors with a flashlight deep inside the female pins for any corrosion or spread pins. What was the original fault here?

And do you have any scan tool communications with the PCM?

How old is the gas in the tank? If it has been a year the gas is definitely bad.

Go through and verify all your Grounds as well, do you have a basic multimeter?

Did you load test the grounds? And how old is the gas in the tank?

Okay, so it will only run for a few seconds then stall out. You don't see any security light flashing or staying on, in the instrument cluster, do you? You also mentioned you replaced the fuel pump as well; did you happen to replace this fuel pressure regulator (diagram 1) it has an internal fuel filter in it. The fuel pressure spec is 49psi, so if the vehicle is starting and stalling, it can be a security system issue or a lack of fuel volume/pressure.
Also does this vehicle have manual or electric door locks? If it has electronic door locks, then it has an Anti-theft system. And if the battery has been disconnected on this security system, once the battery is reconnected the system goes active, if I remember correctly, the security light will flash or stay on for 2 seconds at key on then go out when cranking. But you would notice the light staying on if the system is preventing starting. If the light is on, you could try locking the vehicle and then unlocking it, that should disable any security system if it has one.
If it's not a security issue, you may want to T into the fuel line where you can and make sure pressure is not dropping off.

And how was the vehicle acting with the old PCM installed? Was that causing the stalling or crank no start condition? As for the Odometer flashing, I believe on the pre 2000 models, that means a data bus issue, I've been helping with a 2000 Dodge ram, the last week or so and it was flashing a No Bus message instead, I assume the Odometer is not reading any mileage?

That may not be related to the cylinder misfires you're feeling. Is the instrument cluster working? For some reason there are a lot of these exact Dakota's doing this, you can check the voltage level on pins 3 and 11 of the data link connector, pins 4 and 5 are grounds. You should only read about 2.5volts on either pin 3 or 11, those are the CCD data bus pins, 3 is CCD + and 11 CCD -.
The security light coming back on might be why the odometer is flashing, since the security system (Central Timer Module) is on the CCD network, so you may be dealing with 2 different issues which is common on older vehicles like this.

If the old PCM was preventing it from running at all, and now you're just dealing with cylinder misfires, you'll just have to go back to the basics to deal with misfires, I think this vehicle only has the two fuel injectors in the throttle body, correct? If they are firing good, you should be able to see them looking into the throttle body, they might have some carbon build up on the ends of the fuel injectors as well that's limiting flow. That pretty much always happens with vehicles that have been sitting for a while.
Next check for good spark on each plug wire, and compression testing if needed.
What brand spark plugs did you install? If they are Autolite or a cheap brand, install some good OEM plugs.

Here are a few guides to help with cylinder misfires, and the diagrams below are for checking the Data link connector voltage levels on the vehicles network:

https://www.2carpros.com/articles/engine-misfires-or-runs-rough

https://www.2carpros.com/articles/how-to-test-engine-compression

https://www.2carpros.com/articles/how-to-check-for-ignition-spark