I just bought a new 2016 250, with the 3.2 diesel. First off, I love how it drives, handles etc., and the fuel economy is great, averaging around
21-23 MPG. But I have had the same problem with this thrumming between about 50 and 60 MPH, which gets louder under acceleration, and decreases about 50% when you let off the throttle. There is no doubt, this is from the drive line, nothing to do with tires, aero disturbances, transmission, torque converter etc. Downshifting to 5th has zero effect, so that eliminates everything forward. I suspect the problem lies in their decision to use a three piece driveshaft. Typically, a universal joint is not designed to be operated in a straight plane, it needs to have some angle to avoid a resonant frequency, which I believe is what is happening here with these vehicles. I returned the vehicle to the dealer and another one 1000 miles away in Florida, and got the usual Ford shuffle. "There are no TSB's we don't know whats causing it, we'll contact the factory." Same words both distributorships. Was back again today, as they promised they would "look into it further", but no cigar. That vibration will inevitably become more intense, and start to affect other mechanical systems. I have an engineering back round and have built many machines over the years, and will probably be removing present shafts, add a center mounted "carrier bearing" and run the van with two pieces, as is customary.
My Dodge 3500 with three times the torque, has a two piece unit as do the Ford Pick Ups. The long wheelbase is the culprit, but if the factory won't or can't offer a fix, you would have to accept their findings. Some claim that its a van, get used to it, they are noisy. That's horse ****, those engineers in Detroit need to get working on this, or they may end up facing a class action law suit. Just my opinion, good luck to everyone else with this issue.