Keeping in mind that I've installed what appears to be the exact same package as the OP- My CM-850 Freightliner ECU is completely uncooperative when it comes to ANY mods from the engineered configuration based on the engine serial number.
As of yesterday, I've given up on my new waste-gated turbo and I'm reinstalling the VGT and probably the EGR system as well. Cummins flat out will NOT provide me with a non-VGT program and consequently I constantly throw VGT and EGR codes and am in a perpetual state of derate- I can't pull a 2 mile 6% hill above 45mph. I'm into this engine swap way too deep to back out and switch to a dodge now, so I'm just going to have to stuff all that crap under my hood so I'll have enough power to tow my 30' overloaded trailer.
Since my original post saying it's impossible to convert this engine to a Dodge, I've come to the conclusion that it MIGHT actually be possible. The reason mine would not start was because my injectors were leaking, and I ended up putting in a Freightliner CM850 ECU and it's harness to solve the problem- which didn't help. So now I have new injectors too. It runs and I've driven it 250 miles and I'm VERY happy with Allison (except for the 2-1 down shift wanting to rip out the rearend) which I have regulated via the analog TCM input instead of the J-1939 for the moment. I've built the J-1939 back bone with all the proper Deutsch fittings from Ladd in Ohio, including the receptacle for running a scan tool as would be found in a Semi (took 3 tries to get the right one). OBDII- forget it on the Freightliner ECU, and forget using a Smarty because it will NOT work.
The area of concern for converting the freightliner configuration wiring to a dodge lies in the locations of the crank and cam sensors. If they are different than the freightliner version it may not run. I was absolutely certain of that in my earlier post, but I'm humbly retracting that dogma. At this point, I think it MIGHT work provided you do some other mods. I can't swear to that at this point though.
Swapping front covers might take considerable effort too- the tone wheel is different and I think the crankshaft outside diameter for the balancer is different as well as the Freightliner crank has 6 end bolts vs the dodge has 4. If they are the same, you might be able to change the whole thing over to dodge, but if you do, you'll have no way to control the Allison tranny as far as I know. If the seal size is different, you're in for welding and machining with boring mill accuracy.
The freightliner CM850 ECU that I bought has SAE J1939 multiplexing capability, but I'm not sure if the dodge (I think it's a CM849) ECU can do that.
All I really have to do to make the entire engineered package fit in my 2000 excursion is to modify the outlet fitting that attaches to the turbo (it hits the AC box), modify the down pipe to the much smaller turbo outlet on the VGT, then I have to come up with some creative genius method of installing the damned EGR intake manifold and building a new mounting bracket for the power steering again.
I'm going to try to run this thing with the EGR piping off, but my bet is that I'm going to go right into derate mode again by doing so.
In the end, I think mrod67 is offering some sound wisdom- if you don't want to run a bone stock freightliner Cummins set up, sell it and go with a dodge version. I certainly wish I had.