I own a 2005 Ford F-350 diesel with the factory break controller and the truck has 30,000 miles on it. I use the truck to pull a 36 foot fifth wheel. Recently, a problem developed while I am pulling the fifth wheel. When I have to stop and apply the brakes there is a loud clunk and a slight jerk when the truck's automatic transmission downshifts. It only happens to one of the gears. I am not sure which one. After it slams into that gear, it works fine. There does not seem to be any problem with the truck when I am not pulling the fifth wheel. What could be causing the problem and how can it be fixed.

Dropping and cleaning the pan, changing the filter, and refilling with Amsoil Multi-Vehicle Synthetic ATF or Mobil 1 Synthetic ATF should solve the problem. Downshifts and upshifts improve dramatically with synthetic ATFs. Afterwards, disconnect the negative battery cable overnight, to force the PCM to relearn new shift points.

I only use synthetic ATF in the diesel trucks I maintain for a Texas disaster response team.

Here's how to easily do the work yourself:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-10.html#post1873132

Perform this procedure every 30,000 miles.