Clunk when downshifting pulling trailer

Keep trying it. It may go away as it learns the timing for that particular shift pattern & load scenario. The 5R110 has complicated controls, and takes a bit to adjust sometimes.

FWIW: My V10 Class C's 2005 TorqShift 5R110 transmission failed completely in August of this year after only about 51,000 miles on the RV.

I started to notice something was wrong for a few months by it acting about like what the OP described. Of course near the end in August it did a whole bunch of additional weird things. My mechanics have no idea of why the normally robust Ford 5R110 transmission should fail that soon.

There's only one thing I can put my finger on that may have caused it to fail so soon. Our home lies in the mountains at the end of a moderate-grade long uphill pull and then a steep-grade short uphill pull. After arriving home with the RV I merely shut the engine off. Perhaps the transmission is hot after pulling these grades to our house and I should be idling the engine for a few minutes after arriving home to cool the transmissions down? I've never read anything about doing this .... so am just wondering. Perhaps the OP has the same situation and their transmission is beginning to show early signs of damage.

Check the motor and trans mounts for looseness or separation?

My 2011 (see sig) will "clunk" also. Always at low speed accelerating gently (think parking lot driving). But if I put it in Tow/Haul mode, it never happens. Fluids are fine. Towing or single, doesn't matter. I've gotten in the habit of switching to Tow/Haul when under 15mph.

Computer related maybe?

The trailer is within the towing limits, it has brakes. Both times it was while slowing to make a turn, the ball is lubed. I don't know for sure if

it was upshifting or down shifting. The driveshaft has no lube points on it, on my Pu I removed the shaft and lubed the spline as it did the same

thing while upshifting pulling my heavy ( within the limits) gooseneck. I will monitor it and check the tranny fluid. Friend of mine has been

rebuilding trannys for 30 years, I'll speak to him this week. This V-10 has no issue pulling this trailer or my JK toad, strong motor. The shift

patterns are all normal even under hard accelerations from a dead stop or otherwise.

Happy Thanksgiving guys....

If you pull 4K pounds very often or very far, a tranny temp gauge would be a good tool. Is that weight within the recommended towing limit ??

At this point, I think I would have a sniff of the ATF and consider having it changed.

Having said that, shifts can be abrupt under very specific conditions and usually don't indicate a real problem.

Intermittent problems are hard to track down. Sometimes you're caught off guard when it happens and don't exactly get the sequence down correctly. I think your best bet is to continue to drive it and monitor it for a while to insure you zero in on the issue. First I'd try to duplicate it without the trailer-like Drew suggested it could be some kind of backlash in the hitching or similar.

If you still get the issue and it is a fault in the transmission, it probably will get worse and increase in frequency. If it is still hard to diagnose, maybe your shop has some kind of data recorder you can use. Ford has these tools.

Maybe someone else has had the exact issue and can help..

Downshifted, as in you were slowing down? Or upshifted, as in you were speeding up and it went from first to second? I wouldn't expect any significant clunk on a downshift at those speeds, as there's unlikely to be any significant strain on the drivetrain components—you're using your brakes, most likely.

Is it possible that perhaps what you're sensing is a bit of slop in the trailer hitch bouncing around as the trailer brakes (assuming you have trailer brakes of some sort) and engine braking and motorhome brakes all interact in various ways? Certainly not the only option, but seems like a reasonable possibility to me.

I'm not aware of many if any class C's with locking rear wheel differentials. I may simply be ignorant, but it doesn't seem like a usual option. My '98 certainly has a standard non-limited-slip differential, as I have once or twice found out somewhat to my chagrin.

my spline needed to be lubed

Was it the transmission or the locking rear wheel differential?