[wiswind]

I don't know why it would go out......until after a while of driving.
A flashing CEL is an indication of a condition that COULD cause damage to the catalytic converters......most common being a misfire.
A misfire, that is caused by a lack of spark, can cause raw gasoline to enter the catalytic converter for that bank of cylinders.....causing it to overheat.
There are many possible causes of misfire........dirty fuel injector(s), defective coil pack, defective spark plug wire(s) or spark plug.

One thing that you can do.......to see if it is related to the EGR system.......TEMPORARILY remove and plug the vaccum line that goes to the top of the EGR valve.......take the vehicle for a drive.......does the symptom go away?......if so, then the EGR system is the likely suspect.
If this test makes no change in the symptom, then the problem is not caused by the EGR system.
Remember to reconnect the vaccum line to the top of the EGR valve.
This test should cause the CEL to come on, with a code indicating a lack of EGR flow.......which is not something to worry about......as this test disables the EGR valve.

The EGR valve on the windstar is quite reliable.....however the EGR ports that are mounted in the lower intake manifold are notorious for becoming clogged.....removal of the upper intake manifold is required in order to clean them......A small pick.....or screw driver and a shop vac. is all that is needed to clean them once you get to them
The EGR port is a small 1/4" hole in the intake port for each cylinder......it will be in the intake port without the IMR butterfly (flap).
What happens is that the EGR ports for most cylinders is blocked.....leaving all the EGR flow to go to 1 or 2 cylinders......starving them of oxygen.....causing the misfire whenever the EGR system activates.

Another common issue with the EGR system is the DPFE.....which is the sensor that tells the PCM how much EGR flow there is.....
A lack of EGR flow signal can cause the PCM to open the EGR valve more and more......causing the misfire due to lack of oxygen to the cylinders.