I read about one fix people have done is to update the front end (baffles, airboxes, fan shoud, etc) to LBZ, as well as the turbo inlet elbow to LBZ, then it is fixed for good. Go to maxxtorque.com, and find the magazine issue that covers this, they will give you a parts list, and of course an article that covered the whole cooling issue in general.
It makes tons of sense, and its all GM parts, so i am no longer scared of an LLY, in fact, since it is the last d-max with a manual, i am actually wanting one now.
know two guys that work 3500s a tad hard pulling goosenecks loaded heavy with equipment, and they never had overheating issues with their LLYs, but then again, they left them stock. I wonder if some of the airflow issue is caused by the ol truck being perched up high on a lift, having turbulence at the front axle area, but that is just me.
good luck!