It may be that your friend doesn't quite understand how to use his new scanner.
The transmission has sensors in there to pick up on any alteration in performance from the stock parameters. From my experience with the 4R70W, these sensors are actually very, very sensitive and will cause a flashing TCIL (Transmission Control Indicator Lamp) at the slightest problem. When something is wrong with the transmission, that light at the end of the lever will blink, rather than setting a MIL for check engine.
The problem you're experienceing sounds like an ignition issue to me... Like an intermittent misfire. To back that up, I've recently had similar problems with my truck. On occasion, I would start the engine and everything would be fine till I put it in gear. Then it would begin to shake and want to stall. If I turned it off and restarted, everything would be fine. I'd also feel a sudden, hard jerk from time to time on the highway. I was thinking that the problem was the torque conveter or TCC solenoid.
Today, I checked the spark plug wires and when I got to cylinder #1, the boot fell off the plug when I touched it. The issue with my truck was an intermittent misfire.
Many owners report that the 4.6 engine can go through coils fairly quickly. I'd suggest that you look at all of your coils and plugs. If you are missing on one cylinder as you drive down the road, you can certainly expect that your truck will shake violently.