I am having the exact same problem as you Desiguy91... I actually just took my car into the shop on Friday and they said they had to order some sort of a sensor.. I was in a hurry and didn't look at the paperwork to close, but the part is ordered and should be here sometime this week... I also have a 99 Contour SE sport.
When I start my car in the morning with my remote starter.. I can always verify that it is running, cause I can hear the howling from inside my apt, grrrr.. thats how bad mine is.. and every once in a while it also does the messed up idle thing.. the rpms jump from about 1500 to 500 and just keeps doing that...
when you find out exactly what ford replaces will you please let me know, so that way I can compare what they do to your car and what they do to my car. Thanks in Advance