I just bought a 98 1500 3.9L Automatic. It was sitting for about 4 years before I bought it. When it first starts it idles very rough, shaking the entire truck, but smooths out fairly quickly. As soon as I put it in drive or reverse it starts running rough again, shaking and I can hear the miss. Once I get up to about 10mph it smooths back out for the most part. It has fresh gas, new plugs, intake cleaned, and new oil and filter. I plan to change wires and coil next, I hope this helps, but the conditions of the miss feels as though it's caused by something else. No CEL either.

 

Don't forget cap and rotor. Yeah, they are a pain to get to, do them when you do the wires.

 

Yeah, figure best to do those while I'm already back there. Plugs were definitely due, the insulator around the electrode was black as coal, and they were all between 5-10 thousands over. Still trying to figure out if the unspent fuel from it's current running condition was leaving the mass amount of deposit or if the internal seals of the injectors dried up during it's sitting period and is leaking fuel and that is causing the rough idle. Hard to get a good idea of what to focus on, as I don't know what was messed up before it was parked aside from transmission, and what has gone bad from being parked. Just glad that I don't have to fix any engine wiring, as all the rat's nests were confined to the intake. When I go back to the shop Monday I'll get pictures of the plugs.