OH, Transend=Transynd tranni fluid. You had me going there for a while because I could not figure out what that was. Well, moving on...
OK, I have a Cat 330, Allison 6 speed and an exhaust brake. When I first bought this RV I had the same issues you are describing. It really sounded horrible and I didn't like it at all. What I did was learned to feather the exhaust brake to minimize the jolts. I press on the brake, the exhaust brake light comes on, and then I press on the fuel peddle just a little. That little bit of fuel seems to gentle the braking and reduce the harsh clunking.
Doing that has reduced the hammering to a minimum and I rarely hear or feel it anymore. It still occurs occasionally but not nearly as often.