I just wanted to wrap this thread up with some good news and the fix. After about 6 months of research and troubleshooting, it turned out to be a software issue. The bottom line is that Deutz engine needs to have the throttle pedal calibrated.
Here is a bit more detail on how that went…
A Deutz service center sent out a tech. He had never seen the issue before. He did see there was a software update available for the ECU/ECM, so he updated it and I drove the machine around for about 10 minutes. It seemed like everything was running fine and just as I will pulling back into my driveway to tell him it was fixed, it dropped to “low idle” around 960RPM, and locked out the throttle pedal. I asked him if he could change the engine idle RPM because I noticed that mine always idles around 1200RPM and I thought it should be around 900. He said he can’t do this as this is a low-level setting that he can’t change. I thought that was odd, but he went on to do some more troubleshooting.
He got on the phone with some other techs, and they told him where the utility was located to calibrate the pedal to the ECU. After running through the quick calibration, we restarted the unit, and immediately I noticed that it was no longer idling around 1200RPM. It was running at 960 where it should be. When I saw that I knew that the issue was resolved. I drove it around for about 20 minutes and the issue never happened. The tech on the phone informed him that this procedure must be done on all new engines or throttle pedals. He finished up and was on site for a little less than 2 hours. He then handed me a bill for $1,516 which I was a bit shocked at! I thought this was going to be a free service since I bought then new engine and throttle pedal from them. I am still going back and forth with them about that, but the good news is that the machine runs!