2016 LV3 Idle and Throttle Response issues

Full disclosure, I am not a tuner however I do GM Engine swaps and have over 25 years wrenching on GM's. I am currently working on a 1946 Jeep Crawler project with a 2016 LV3 4.3. The customer purchased a ECM and Harness kit from a company that is not new to the harness and tuning world, but i will leave their name out of this at this point. I am not the original installer of the wiring or ECM, but i am the first to work on this Jeep and actually get it to run. It came to me with bad grounds and the MAF sensor installed in the air tube backwards. At this point I am having idle and throttle response issues with no codes. The Tuner claims that the ECM is running a factory tune with no changes other than deleting the required parameters to delete VATS, the Variable Displacement Control, Canister Vent, Fuel Pressure control on the supply pump, and probably some other things I'm leaving out. The supply fuel pressure is set at 70 PSI per the Tuners instructions. Sometimes when the engine is cold started it will not idle, it will start and die, or blubber below the idle target with some idles speed flares like it is searching for throttle blade position. I can see the movement of the throttle body position sensor on the scan tool and it seems to correlate with RPM. The fuel seems to be rich with negative trim numbers on the scan tool. When I push on the throttle pedal the engine speed is very slow to respond, and will flare higher than it should in relation to pedal position and then take a very long time to come back to target idle. Other times I cold start it and the idle is completely normal, coming up to about 1000 RPM and within a few seconds coming down to the 675 target and idle like a dream. When this is happening and I touch the throttle pedal the engine speed will start to steadily climb and within 10 to 15 seconds RPM is approaching 3000 RPM. While this is happening the throttle body position on the scan tool climbs in correlation with the engine speed starting at 16% at idle and climbing to about 30 % at 3000 RPM all while pedal position is at 0%. I get no throttle correlation codes when this is happening, and i don't know if there is a ceiling to the RPM climb because I have always killed the ignition at about 3000 RPM. I have verified powers and grounds to the ECM and at this point I am a little stumped with what is going on. The Tuner will not entertain the possibility of a ECM malfunction, however with the multiple and random problems I am having with no codes presenting I am leaning toward a ECM issue. I would love to hear you guys thoughts as tuners with this situation. Thanks so much in advance.