I have not tried this yet. Why would the ecm be damaged

This is maybe what is going on. I'm thinking your new harness is for a 3 and your ECM is a 1.
That said, I took my 1 harness, and did plug it into one side, very gently into my 3 ECM. Don't have a 3 harness other then whats on the boat and not going to try with it on the 1 to verify

I also compared my mefi 1 and 2 spare ECM's and the pin out looks the same (32 pin connectors). So if your harness is missing keys which keep a 1 from plugging in, then it would happen without knowing with my limited knowledge

From my research which is talking several marine tuners it is possible to “ go from 1 to 4 and 4 to 1.

Basically going from 3 to 1 would require changing the knock sensor and FPR pins and connector. I still have my old harness which should make things easier.

Hard to comment in great lengths but for a jist MEFI 1 does not even have the same circuits pin outs nor the J connectors per those compared to MEFI 3.

This is how the ecm can surely be can end up being damaged and I still do not see how you connected the ecm from a mefi 3 harness to mefi 1 and the engine starts and runs ???

HERE IS PRIME example how off base this is for just example.

THE IAC for mefi 1 and MEFI 2 is J2 - 28 and J2 - 13 and J2 - 14 and J2 - 29

The IAC for MEFI 3 is J1 - 28 and J1- 12 and J1-11 and J1 - 27 not even close for connections and pin outs in the ECM for jist of an example.

Do you have a service manual for this per what you are trying to do ?

Bup

You are way more knowledgeable than I am. All I did was call a few tuners and the tuner at AZ speed told me he would sell me a diagram on what pins to change to use the Mefi 1 ecm.

Another tuner Hardin Marine suggested not doing that.

All Dodge is willing to send me a mefi 1 harness if that was your 2 best choices Which way would you go?

This is what I was sent. Will it work?
https://cimg8.ibsrv.net/gimg/www.off...932ae3460.jpeg

Looks like some great info and I'm sure it can be done IF followed

Keep in mind you'll need something (tool) to unpin and swap pins in the connectors