Weird AGG problem

Had my JX to AGG conversion a month or so ago and have now started to build up confidence in the new arrangement and going for longer trips. Have now completed three 200 mile plus trips and have a consistent problem occurring. Engine runs really well to start and has really transformed to driveability of the van but this one is doing my head in.

All is great for about 130 miles of motorway style cruising at 60-65mph. Then we start to get a stutter in acceleration and significant power loss around 2800-3200rpm. speed drops and you need to change down, speed still drops. Heavy right foot  and it will, in time, push through the issue and recover power and revs, but as soon as the revs drop we are back to a judder and decreasing power. Oil pressure is stable at 5 bar and coolant temp is stable at just touching the LED on the temp gauge.

My thinking was that it cannot be mechanical since the engine performs flawlessly for the first couple of hours, but the problem is consistent now over several trips at 130-150 miles. Even though the engine has been at operating temperature for a couple of hours I thought it might be temperature related but fuel pump is cold and ECU casing is stone cold.

Now the weird thing. Stopped at service area for a quick bio break and restarted and problem has gone. Engine pulls seemlessly through 3000 rpm and had no further problems for at least 50 miles (haven't got beyond that yet!).  That seems to rule out temperature, since the engine cannot have cooled that much that a reoccurrance wouldn't have happened within 10 miles or so. This is doing my head in!!

I am an IT guy and this has all the hallmarks of some crazy stack overflow in the ECU - had so many errors that my buffers are full and I am going to do weird shit! Turn off the power and everything goes back to where it should.  But I don't believe the ECU works that way. Surely some sensor cannot get that clogged and then magically clear itself in a few minutes?

Any thoughts before I go visit my local VW (independent) dealer and get them to connect the magic diagnostic box? I don't yet have a real time diagnostic cable that I can connect. Even with it I'm not sure the boys in blue will take kindly to me checking the laptop screen at 60mph on the motorway!!

All suggestions and thoughts/ideas gratefully received.

Thanks in advance

Steve