Truck has 7k miles I thought it was an mds issue but I've been driving locked in 6th +\- and clunk still happens. Motors mounts were changed but that was for the mds vibration which still is same. I guess it should go back to dealer again.... so annoying. Truck is pos
I know you're frustrated and on the Power Wagon Registry I brought up this same issue earlier last year, as a few of our 14+ PW's were doing the same thing. Truth is, there is no solution but time and a change in driving style. The throttle/timing/fuel mapping in the tune is for economy, yes, economy in a 6,700-7,000lb 2500 series 6.4 that isn't even obligated to state the EPA rated MPG on the window sticker. I tried all the fixes here, and originally thought it was MDS, but like many the issue still remained in manual mode with mds disengaged. Bucking was the worse under 1,600 RPM and with a high load (as it doesn't like to downshift). The engine just is not mapped properly with a low throttle position at those speeds/rpm. It makes no difference with octane, I originally thought it may be pulling out timing but it made no difference with two fillups of 93.
My PW now has 23k miles, the problems such as the physical/audible 'bang' from the mechanical engagement/disengagement of the front axle to transaxle assembly (to save fuel economy while cruising) is no longer their (I could feel it through the pedals before). We've concluded that this 6.4's tune is very susceptible to minor variances in fuel composition (moisture/ethanol content). 87 octane is fine (once again, no difference running 89-93), but I've always had luck with newer stations that quickly cycle available fuel storage (meaning, busy ones). I've tested this theory no less than 10 times, fueling at other less frequented stations and the truck starting to buck/hesitate again. It's so noticeable, my wife even comments and knows where I've fueled without telling her; we carpool with it everyday. For the past six months I've been using the same three stations and the truck has very little to no symptoms anymore.
What I've learned to do is also immediately place the truck on tow/haul mode when driving, turn off tow/haul above 50mph. No difference in fuel economy, and no bucking/hesitation. If you like to 'putt around', turn on tow/haul mode.
That is why people who invest in a tuner/new ecu state how great the truck is after. It no longer holds gears, disables MDS, and limits shift points. The engine is mapped properly, running smoother and more efficiently at lower RPM. If you don't want to invest in a tuner, then the tow/haul method is your best bet currently. The truck just needs more miles to break-in, mine drove me insane originally as well. Hope this helps!