possible timing problem

I have a 04 Dodge Ram 3.7, and I just replaced the right cylinder head because the #2 rocker tower was broken, prior to removing the timing chain I set the crank to tdc to insure the other two chains would stay in time. When replacing the chain I set the cam sprocket at 12:00. The truck idles really rough, no codes, or misfires on the monitor but the temp. sensor is only reading outside air temp and so is the gauge What could that be caused by and is it possible that the ECM needs to be relearned on this 3.7 because of the rough idling? I am puzzled This far from my first timing job but it does make me feel like is. Help please