Steve,
I had a 97 3500, 12 valve, auto with a PacBrake on it for nearly 70,000 miles towing a 5th wheel at max GCW all over the western US--no problems. I had a manual switch to hold it in torque converter lockup when using the PacBrake. The only disadvantage is once you put it in a gear(3rd/direct, for example) with the TC locked, you were "stuck" in that gear all the way down the hill.
The problem is that a large amount of heat is generated in the transmission with the factory torque converter unlocked with the exhaust brake on. When ever you take your foot off the throttle, the torque converter unlocks unless you override it. That's why it isn't recommended to use an exhaust brake on an auto trans truck.
If I were you, I would talk to Bill K about possible transmission mods for using an exhaust brake since you already have some of his products in your transmission.
Bill