Yes the valve cover has to come off as the cam has to be "zero'd ". What manifold are you talking about, which motor do you have? Is it even a diesel and not a 2.0 gasser ?
There are at least 4 or 6 in the back attaching a brace to the head.
On the crank pulley there is a groove which lines up to an arrow on the timing cover. On the cam there is also a groove but square.It lines up to the "OT" mark on the cover behind the cam gear when the belt cover is removed. Then line up the distributor as i said before. Pay close attention to the tensioner and the direction it adjusts to. Some gasser tensioners turn down ;counterclock wise] rather than up [clock wise].