I am just guessing here, but it could be a bad throttle position sensor. I recall having seen a posting somewhere (how is that fro a scientific notation?) where a guy had trouble with a Miata and hacked the throttle position sensor. He found corrosion internally.
So maybe somebody with that problem can put in a known good TPS and report back.

 

I am guessing that it could be a fuel delivery issue. Plugged filter, dirty injectors, bad fuel pressure regulator.
It could be a problem with the EGR system.
Vacuum leak.
I am thinking that not all miss fires are caused by the ignition system.

No one specified if all cylinders missed or only 1 or 2. I assume all of them missed.