Another thought. You mentioned using a scantool to check for diagnostic codes, but have you tried looking at parameters from the onboard computers while the issue is happening, to get clues to what the car is 'thinking' or trying to do?
Such was the approach I took when I was chasing my own transmission gremlins, which had the car balking or shunting in gear changes, but was intermittent and generally didn't record any error codes. So I set up an arrangement to monitor and record various parameter values from the ECM,
TCM etc during general driving, to try to get an insight into what the computers thought they were trying to do. (For specifics I used an OBDLink MX linked by Bluetooth to my smartphone running the mobile Forscan app; not sure if you can achieve similar with your device.) You can read about my experience at the thread here:
http://fordforums.com.au/showthread.php?t=11452297
For example if you want to know if the car is doing a DPF regeneration when you experience the rocking sensation, that is easily confirmed if you can view a live readout from the exhaust temperature sensor (which will go up to 600°C while the system is burning off the built-up soot). If you suspect it's the gearbox rowing gears, you might be able to get some evidence for this if you can view some of the
TCM parameters for the gear shift intention. In my situation, it was a classic case of the faulty gearbox input speed sensor, which was evident in the graphs I made below of some of my recorded data. The red "RPM" line represents the reading of the gearbox sensor that was going bad, in the highlighted regions you can see the trace going crazy which corresponded with the car balking or lurching as the other drivetrain systems couldn't tell what was going on.
