the first thing that springs to mind is an engine management calibration error, there was a concern with the minimum drive pulse of the injectors. With a reduction in the minimum drive pulse the fuel delivered doesn't meet the amount of fuel demanded as a consequence of this the engine management doesn't detect the engine as running usually the lack of throttle response is between a couple of seconds up to 3 minutes.
To cure this the latest calibration level available for the engine management needs to be downloaded into the PCM, the software number depends on the engine emission level, power output and transmission. For example a 130PS stage IV 6 speed transmission needs to be at 5S71-12K532-SE or higher, these calibrations were released in late 2006.
To update the calibration has to be done by a garage that subscribes to software updates, I personally would recommend Ford IDS to do this as this is checked and updated daily if required so will always load the latest software for the car.
It is possible there is a throttle pedal concern but this is very rare on this model and usually would result in a warning light showing.
Start with the software as this is a known issue which is why Ford released the updates originally.
Let me know if I can assist further and I'll reply as soon as I'm able to.