I will add my recent experience with this. My Flex was off the road for quite some time because of really bad shuddering. The dealer diagnosed as a failed torque converter, 140k on the odometer. I installed a Ford OEM reman torque converter, a used transmission with 60k miles with solenoid pack and a new valve body. Upon initial drive tests, I could see my RPMs fluctuating up and down and also feel surging when in a high gear with torque converter lockup and at around 45mph. I confirmed with the Forscan application that the target torque converter clutch slippage was 20rpm, but in fact, I was getting fluctuating slippage up to about 100 rpm. Knowing all my transmission parts were already replaced, I began to suspect an engine issue. I checked my EVAP solenoid on the engine for vacuum leakage, but it was fine. Forscan was showing much higher long term fuel trim on Bank 1 than Bank 2, about 10-14% versus 6%. I started to suspect an issue with carbon on my fuel injectors causing the problem. I ran the fuel tank down to about 1/2 a tank and then put in Techron Complete Fuel Injector Cleaner good to treat 20 gallons, and then idled the engine for about 45 minutes. I then took it for a 10 minute drive, filled the tank with Shell Super gas, and then took it for another 60 minutes drive with multiple speed/rpm scenarios. By the end of the drive, the fuel trim was starting to come down, the torque converter slippage was substantially reduced and overall driveability improved. My scans with Forscan during the 60 minute drive show the torque converter slippage greatly improved.
Bottom line is that this experience seems to validate what I had suspected. Fluctuating RPMs during torque converter lockup at high load/low speed/low rpm scenarios (e.g. going up a hill in 6th gear at 45 miles/hour with torque converter clutch engaged) can be caused by fueling issues and in particular what I think must be carbon buildup on the fuel injector. If you are having these symptoms try some top grade PEA based fuel injector cleaner and see if it helps.