When diagnosing a cylinder head gasket failure, it is highly recommended to measure the liner protrusion. Measure the liner protrusion at four locations, 90 degrees apart at each cylinder head. If the liner protrusion is below spec(0.001″) you have counterbore damage. At this point in time there is no repair for counterbores, the entire block will need to be replaced.
I now have a machine to cut the counterbores on DD15 engines, for S/S shims. I can machine them, with the engine still installed in the truck.