I can get the ECM/PCM replaced on a part's warranty

I would just replace the ECM/PCM with the parts warranty for now.
The "new" ECM/PCM they installed may have been a new remanufactured part. Many of the expensive electronics (e.g. ECM/PCM) are sent back to the manufacturer for rework and then put back into parts stock inventory. If the part tested as NDF (no defect found) they do not perform any repairs ... they just put it back into parts stock inventory. If the same part cycles through the rework process two or three times, and still tests as an NDF, they scrap it.

As input signals to the PCM change, the PCM adjusts its response to the output devices. So I'm not surprised that your car runs better once warmed up.
The PCM operates in two different modes: Open Loop and Closed Loop.
During Open Loop modes, the PCM receives input signals and responds only according to preset PCM programming. During Closed Loop modes, the PCM will monitor the oxygen (O2S) sensors input.

Ignition switch On, engine start-up (crank), engine warm-up, acceleration, deceleration and wide open throttle modes are Open Loop modes.
Idle and cruise modes, (with the engine at operating temperature) are Closed Loop modes.

The NAG1 (5-speed) electronic transmission has a fully adaptive control system. The system performs its functions based on continuous real-time sensor feedback information ... including information from the PCM.
If the information from the PCM is not correct than the transmission may act up accordingly.

Bottom Line: try the free PCM replacement and see if you still have transmission issues.
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Thank you for the response djalbin! I'm just hoping (but not expecting) a small miracle here. Your post has reduced my stress level a bit.

 

Quick Update:

Got my car back yesterday after the dealership (upon my orders and against their wishes) only replaced the ECM/PCM under the part's warranty. It took a couple of days to get the car back after the repair due to test drives. Drove fine the day they replaced the computer and the next day. Then they wanted to drive it first thing in the morning. Still good!

I've had no problems today driving the car. Still too early to claim victory but it seems a faulty factory issued replacement computer was the source of my problems (with the stalling and acceleration). I just find it very funny that both shops refused to believe that the issue was the computer. The first shop wouldn't order a second new computer and replace it and the dealership saw it as a minor issue compared to the major issues they found (TCM, Torque Converter, Transmission).

I'll give it a week but so far so good!

 

My wifes old 2006 300 would throw dummy lights each morning, stall, then drive fine for the rest of the day....we fixed it by replacing the gas pedal....there is some type of apps sensor in the gas pedal for these cars and that fixed my issues like you have above.....best part about it, it was not an expensive fix at all......thank me later!

 

Update - Well, 5 days later and the problems are back. Came slowly and only in the morning (again). Now the problems are more consistent to the point the car cannot be safely driven. No codes just the check engine light and ETC dummy light. Problem goes away as quickly as it comes.

I still think it has to do with the ECM/PCM (maybe the wiring to the unit). I would love to run the car without the PCM using the sensors. Can it operate on factory default settings (if there is such a thing)? I mean I can reset the PCM (and have) but the problems return quickly.

 

You stated the dealer thinks its also a TCM problem,so why are you ignoring that? It could be if the TCM is bad and when you come to light and it stalls,it could be that the torque converter is still locked up.Your car wont run with out PCM.If your not using a scanner,you might not be able to read Tranny codes.

 

This sensor code problem is very stressful and Chrysler dealer repair isn't easy to believe. My problem is lengthy also So here we go. CEL came on one morning at first start of car(2008 charger 2.7) took it to first dealer test results all sensors bad and oil pan leaking at the drain. 1400.00 to repair all. Passed and paid 100.00 test fee. Replaced all myself camshaft,crankshaft and all 4 oxygen sensors (Bosch brand) had codes reset. Drove about 2 miles came back on. Tried that 3 times same results so took it to second dealer in the area (CEL still on) for second test. Tech said not OEM sensors need to replace with NTK brand wanted 700.00 to so that. So passed again paid 100.00 test fee and replaced them myself. Had codes erased and CEL came back on instantly soon as I starting it. Still reading bad o2 sensors all 4 of them. I'm out of ideas. Anyone else have anything?

 

Tech said not OEM sensors

Not using OEM sensors is a problems because the non-OEM sensors are not calibrated to perform the same as OEM sensors.
So what DTCs are being logged now?
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Still reading 0032,0038,0052,0058. That's with the new OEM sensors already installed.

 

0032,0038,0052,0058

I assume these are all "P" code (e.g. P0032)

P0032-O2 SENSOR 1/1 HEATER CIRCUIT HIGH
P0038-O2 SENSOR 1/2 HEATER CIRCUIT HIGH
P0052-O2 SENSOR 2/1 HEATER CIRCUIT HIGH
P0058-O2 SENSOR 2/2 HEATER CIRCUIT HIGH

Either the O2 sensors are bad or the connectors/wiring is bad.
HEATER CONTROL CIRCUIT OPEN
O2 HEATER GROUND CIRCUIT OPEN
O2 HEATER CONTROL SHORTED TO BATTERY VOLTAGE

Is there any corrosion on the connectors, frayed wires, etc ... on the connectors/wires attached to the O2 sensors?
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O2 Sensor