Thanks for all your interesting responses and discussion. And thanks for getting back on topic.
I want to remind you all that there is an autoscan posted on page 2. I've also posted on page 2 a controller map of my car running poorly when cold as well as a controller map from a properly running car. They were both recorded at the exact same coolant temp, 37.8C.
I'd also like to reiterate some of the most significant observations (at least to me) of this most frustrating puzzle:
The car ran fine before the manual swap AND it runs fine after the coolant temp rises above 56-58C. So whatever is causing the issue resolves itself when the car is warm.
When the car is cold there is ZERO throttle response despite normal functioning of the . When the car is warm the throttle runs properly and the engine revs smoothly to redline.
Despite all the discussion I'm confident that both of my ECUs are functional. The stock with the Immo delete works perfectly when installed in a normal running Passat B5 TDI.
When the car is cold there are some significantly abnormal values when compared to the control car. I'm not implying that these are the cause of the problem, only measurable observations using the controller map function. The first number is my car the second number is the control for comparison:
RPM- 651/ 861 (RPM slowly increases as the car warms)
Injection Quantity- 33.8/ 7.4
Specified MAF- 665(sometimes 850)/ 285
Actual MAF- 430/ 280
Ignition Timing- 13.6 BTDC/ 3.1 BTDC
Duty Cycle- 100.6%/ 79.3%
And there are many more differences but these are the ones that caught my eye.
When I first start the car cold it will start immediately, idle smoothly for a few seconds then suddenly increase RPM up to about 900-1000 and then suddenly try to die. The first few times I start it, it will actually shut down. After a few attempts it will just barely catch and settle into a very slow and rough albeit persistent idle that allows it to warm up enough to run normally.
I have tried disconnecting the MAF sensor and tried a MAF sensor from a normal running car. I have also disconnected most of the other sensors including the camshaft position sensor, coolant temp sensor (replaced with a new CTS from the dealer), O2 sensor. I've also cleaned the valve a tried disconnecting it and the ASV. None of these have made any difference. I've looked for misplaced rags in the air intake path and checked the fuel system. I have NOT measured tandem pump pressure.
When I pulled the engine I replaced the plastic coolant manifold, thermostat, CTS, and crankshaft position sensor. While the engine was out I did a BSM delete and installed a new timing belt and water pump (I just rechecked the timing belt for proper alignment). I also installed new fuel and air filters.
The manual transmission is an FHN from Dutch Auto Parts and all the other swap parts were form a B5 6 cylinder gasser. I modified the wiring for the clutch start switch, the cruise control, and the reverse lights. The is removed and the connector is sealed.
Again, many thanks for your thoughts and comments.