AnthonyT

Thank you mr Anthony, all went well.

What Jay said is mostly true, but there seems to be an exception on some early transponder optional vehicles. There's a function in the J2534 toolbox that comes with the Drew Tech and rebranded Drew Tech tools to turn off the immobilizer. It doesn't work most of the time, but did work once for me on a Durango. I can't remember what year it was though.

Update. Added skim programmed key car starts and runs. After plugging in the skim and turning the key on the security start flashing in the the dash. Then did a skim vin edit , program key , transfer secret key car starts and runs. Thanks.

Update. Added skim programmed key car starts and runs. After plugging in the skim and turning the key on the security start flashing in the the dash. Then did a skim vin edit , program key , transfer secret key car starts and runs. Thanks.

If the PCM came from a donor vehicle that was immobilizer equipped, you will need all related immobilizer components from that donor vehicle to create a running vehicle on your end. Nothing you can do to that PCM will revert it to non-transponder. Add the cost of transponder keys, labor, and programming, of course.
As an aside, I've had a couple of shops call me that have installed boneyard columns on non-transponder Chrysler vehicles. The replacement columns they sourced, came with SKIM modules from transponder equipped vehicles. They unwittingly made all the available connections and attempted to start the vehicle.
At that point, what was once a non-transponder PCM, was instantly and irreversibly transformed into an immobilizer PCM.
To any naysayers who may question the validity of these statements, I realize this may sound preposterous. But yes, it's entirely possible and completely factual. If still in doubt, I implore you to conduct your own field tests and report back here with your results.
Edit: When I said, "you will need all related immobilizer components from that donor vehicle". I meant that you will need the remainder of the immobilizer system components. Not necessarily those components directly from the PCM donor vehicle...

I was at a shop yesterday to make a key for a different vehicle. While I was there they asked if I would take a look at this 2016 Honda Civic, the immobilizer light was flashing and the vehicle wouldn’t start. I walked over to the vehicle and saw they already had their Maxisys Elite connected, so I thought great I don’t need to get mine since that would be my tool of choice for this scenario. I didn’t get any info and I didn’t really ask any questions because I wanted to make an initial assessment so I knew what questions to ask. 
I want to share the diagnostic process I used to repair this vehicle thinking that it may help others. 
The first thing I did was go into immobilizer setup and attempted to perform an “all keys lost” programming. I was pretty certain it wasn’t going to work but I was looking for a specific response from the vehicle. I got what I was looking for- “immobilizer system not normal” if you get this message you can try to program the keys as many times and with as many different keys as you want and it will never work. 
Next I grabbed my antenna tester out my pocket and tested the immobilizer coil. It was putting out a signal. 
After that I went to diagnosis and did an auto scan on all modules. There were no codes in the ECM or immobilizer system but there were codes in the ABS/TCS/VSA, EPS, and a few other systems. I started checking the codes in each system one by one. I would read the codes, clear them, cycle the Key, and read them again to see which ones came back. 
The ABS system had a hard fault for “internal failure”. I ask the technician if he had checked the ABS system. “Oh ya, I put a new ABS module in it.”  Did you run the replace function in Immobilizer setup?  “What’s that?”
Then I went to the main screen on Maxisys, selected hot functions, then Immo, then immobilizer setup, then MICU,VSA replace. I followed the screen prompts and when I was done the immobilizer light was off and the vehicle started. After that I went back to the ABS system cleared and rechecked codes. Surprisingly the internal failure code was still there but my job was done. 
Normally I wouldn’t even take a job like this, the only reason I even looked at it was because I was standing next to it and they already had their Maxisys hooked up to it. If you’re going to tackle a job like this you need the right combination of tools, knowledge and luck. As the saying goes sometimes it’s better to be lucky than good!  
The only thing better than fixing somebody else’s car with your Maxisys, is fixing somebody else’s car with their Maxisys!