250 Engine Runs Terribly Redux

I just heard from the auto shop machinist. He told me that all 6 cylinders hold a vacuum perfecty, the spring and valve stem heights are ok, and the head was milled within specs. His opinion is that water is getting into the cylinders because the head wasn't torqued down correctly. He points out the water stains on the newly machined head surface as proof. I also asked him yesterday if water could be getting into the cylinders. He also told me that since just the exhaust valves are black the valves must be seating correctly otherwise both the intake and exhaust valves would be black. I had questioned if too much metal was milled off the head. His recommendations are to clean and run a die on every head bolt and put a tap through every head thread on the block. I just now did everything he told me to do. The machinist told me that after I reinstall the head I shouldn't have any more problems. I'll pick up the head tomorrow morning and keep my fingers crossed.