Haven't had this problem on my Dodge, but my Mazda was doing something similar. I thought it was the injectors, so I replaced them, and she ran a little better but still felt like it was missing.

I ended up changing out the fuel rail - the injectors didn't look like they were seated evenly, and after reseating them on the old rail with no improvement, I got a replacement rail and they finally sat correctly. Engine runs smooth now.

Not sure if this is your problem, but I thought I'd suggest injectors.

 

Fuel, Spark, and Air, the fire triangle.