Hi,
If you are positive you haven't got an issue with the ignition system then I think I would be looking at a possible air leak.
If the car were mine I would check the pipes are clear and intact that come off the back of the rocker covers and go to the large plastic elbow shaped pipe under the MAF, and remove the throttle body and replace the O ring seals either side of it, and give the throttle body a good clean with carburettor cleaner while its off.
I also can,t help but wonder if there is possibly a fuel pressure issue, as there is a vacuum operated valve on the fuel rail if this wasn't operating correctly/sticking might cause slow running issues and as it is vacuum operated when the rpm rises the increased vacuum frees it, just a thought.