When you removed the engine , you did disconnect the battery, yes/no ?

The shift points were lost and now have to be relearned.That is the fun of simply disconnecting the battery.

Yes, The battery was disconnected for about 2 weeks. I have driven the car for a week twice a day to allow for a drive cycle cool down period. and still the warning comes on. i also have a p0017 (Crank Senor/Cam sensor out of correlation) code. as well as a couple others. In all my years of working on cars i have never seen such a common debilitating problem on a specific car. From my research i have found this is a german engineered engine package (Which explains a lot of the bad engineering). I am now thinking it is a TCM/PCM reprogram issue. Does anyone have any useful input on this or other fix ideas. Thanks in advance.