Need a bit more info:
What do you mean by, "head bored out?" You mean the head was just cleaned up really well, did you shave down the head, opened up the combustion chamber bowls, port matched the head, etc.?
Any other codes along with the P01349 code? Verified that the timing was set right when you changed the chain? Reset the VVT sprocket per FSM directions? Have you put a data logging scantool to make sure the timing is changed (intake overlap) depending on engine load and speed?
P01349 is a pretty straightforward DTC, it only gets set if the timing does NOT change when the ECM expects it to be, or if the timing appears to be fixed. Car will still run pretty well if the timing is fixed, so hard to tell VVT-I operation just by driving it - need to put a scan tool on it. Could be an issue with the OCV (solenoid could be moving, but not enough), bad ECM (wiring issue, missing chassis ground or RF noise suppressor, etc.), or could be a chunk of debris got caught inside the VVT vane inside the sprocket, or if it got "locked" in the wrong position during reassembly.