Acceleration bump type problem

2004 Passat TDI and in general I like it. Quiet, good response-sporty driving, great pickup for the little turbo engine but:

At about 116,000 miles the Check Engine light illuminated and the message stated see the dealer for an emission problem.

I brought it to the dealer and the Diagnostic Trouble Code, PC10101, indicated it was the Mass Air Flow Sensor which they replaced. However, after leaving the dealership and within a few miles the same indicator illuminated.

I returned to the dealer. This time they determined the turbo cooler had a crack and replaced that. Sure enough within miles of leaving the dealership the same indicator illuminated. This time they kept the car for 2 to 3 weeks trying to isolate the problem, even calling the regional VW guru mechanic. He too was at a loss for a solution let alone the problem. Eventually, they found a vacuum leak in a turbo hose, replaced the ?O? rings and the problem went away.

Recently, I have been experiencing a bump type of action when accelerating, a moderate acceleration, between 60 and 65 mph. I describe it as a bump because the first time I looked in the rear view mirror thinking I was bumped. It was not a hesitation in the transmission. It does not occur every time but I have been able to replicate it occasionally by dropping speed to around 50 mph and then accelerating.

I took it to the dealer and guess what the diagnosis was. Yes, the Mass Air Flow Sensor. They replace it. Said they test drove it and no problems. But when I drove less than 3 miles accelerating onto the interstate the same bump feeling occured. It may be starting to appear at other speeds.

The game plan is to reprogram the TCM. If no solution then flush the transmission and the last step is to drop the transmission pan and inspect the transmission.

My questions are these. What do you think the problem might be? Is the game plan reasonable? Why is the Mass Air Flow Sensor always reappearing as the cause and could this be an indicator to what the actual problem is?