I have a 1998 Taurus SE 24 Valve that had the same type of problem you described. As I have been back and forth with a couple dealerships to cure a performance issue, one of the latest service bulletins related to the computer programming cured the problem you described, unfortunately not the issue I have.
You may want to contact a nearby dealership and see if there is a recall or service bulletin for the problem you described. I was not charged for this bulletin, although this was also performed during a follow-up visit to the injector cleaning that did not cure my problem.
Best of luck,