No communication with reader

More then likely it has failed. This is what is called and SCI bus so we can try and check for voltage at the PCM on all your ignition feed and grounds. If they are all good then we can check for continuity between the DLC and PCM to make sure you don't have a wiring issue.

https://www.2carpros.com/articles/how-to-check-wiring

However, the fact that this just worked, I suspect you are correct that it is a controller issue.

I attached the wiring and connector info that will help with this.

Thanks.

Normally the 5 volt supply will not cause a scan tool to not communicate. So if you don't have a 5 volt supply then we can dig into that on a new post but let's try and stick with why the scan tool won't fire up.

Do you have 12 volts at the DLC on pin 16? If not then we need to check the fuse as that is likely the issue.

Correct. The 5 volt reference comes from the PCM on 2 different connectors. However, this is what all the sensors use to send the signal back to the PCM so it knows what each sensor is reading.

What type of scanner are you using? It is just odd that it will not communicate with the PCM when you are missing a reference signal but have power and bus communication. Also, which 5 volt are you missing? Which PCM connector? C1 Pin 17 or C2 Pin 31?

That isn't a transformer, it is a choke, basically one single winding, if you have 5 volts on one side but not the other it has opened ie the wire broke. From that image it looks like you had water get into the box and corrode the components. It might be repairable if you can remove the potting compound and deal with the surface mount parts. Do you have a microscope, hot air reflow and mini tipped soldering station?

That will make it tough to repair that ECU as the components are very small. There are places that will rebuild them but you could likely get a used unit reprogrammed to fit your Jeep for less. I normally reserve a rebuild for ones that are either super expensive or no spares exist. The reason there is no com with that ECU is likely because the 12 volts is there to power it but most of the internals operate off the 5 volt buss along with the sensors. It's also likely that the 12 volt feed has a similar issue of corroded parts on the board.
If you would like to see the way these boards can be tested and repaired take a look at Maic Salazar Diagnostics and L1 Automotive Training both have a few videos on tracing the faults and repairing at board level, might give you an idea of a way to proceed.