If it is rough starting and then "smoothing out" then the engine is not running as it is supposed to. That may not be a "miss" but it is deffinately not running right. I had the exact same shaking symptom when my seperator and ICV messed up my fuel trims. Wife said "the car is shaking!" and it was because it was leaning out so badly it was about to stall at idle.

This is spark or fuel at idle. Did you by chance make sure the plugs are not loose, and that all your ignition wires are tight and the grounds to the coils are tight and clean?