The head must be measured accurately. Allowable warpage is generally only .008 per linear foot. Be sure to check the top of the block also. I have seen them warped a lot. A warped deck will also affect your line bore. I never found it worthwhile to try to true the deck on a warped block. Also, was the head torqued in the proper sequence. GM always recommended retorquing head bolts after run in. This means only trying them for proper torque not backing them off and retorquing them. Unless the engine is very high mileage, there is usually a reason. Especially if you had zero compression on adjacent cylinders.