I have a 2004 3.9L, the codes codes they give although maybe helpful, are generic. Did you gap the plugs, as plugs out of the box are off, some a lot? When you changed them, were they clean or covered in deposits, my 3.9 has been using oil, so mine get so much deposits, that it fouls the plugs. Mine would run perfect several days in a row, then missing and running bad, then running good for several days, I thought I had gotten a bad tank of gas, so I did like you, but it turned out to be 3 fouled plugs, and I think I only had about 10,000 mi on them. You also could have a bad coil pack (it is actually like 3 coils in one package), but each coil fires 2 cylinders, or the module. What I would do, is pull the sparkplugs, one at a time and check them, if okay, then put it back, if any are bad, then replace them all. My 2 cts. Good Luck.