It may make the harmonics rough but I fail to see why it would miss when the R's pick up.It would back fire and all kinds of other stuff if that many plugs were wired wrong even at an idle. The ticking in the timing cover along with missing at off idle makes me really suspect the fuel pump. Even new, these can go south. Try to find a fuel pressure gauge and see what happens when you hit the gas. Just a thought.Best of luck.