Believe me, I had a similar problem on cold start ups. I would get the CEL during warm up and notice as I was decelerating, I would get a slight hesitation and then the engine would start bucking and the rpm increased upon stoping and settled back down to 700. I changed everything I thought was connected to electrical and still could not figure it out. What I finally did was take the truck to a reputable mechanic (which I thought I should have done to begin with and saved myself some $$$). This is where it gets weird. He changed out my thermostat and the CEL went away and the engine started running smooth upon acceleration/deceleration. Apparently the computer was not getting the right signal that the engine was at operation temp and would overcompensate with a richer fuel mix.
Go figure/worked for me