1999 Mercury Tracer - Rough Idle?

I have a 1999 Mercury Tracer, 2L Engine, 80,500 miles that has developed a rough idle problem, that has caused the "service engine soon" light to come on. It appears to be missing, as there is a lag upon accelleration. When this happens the "service engine soon" light begins to flash.
This problem appeared after beginning to hear a clicking noise, when the car was taken in or out of gear with your foot on the brake.
No mechanic will give me the same answer. I have been told by one mechanic that he would been to do a tune up first, then put it on a the diagnostic system at a charge of $280, with no guarantee that it would fix the problem. Another told me that it is in the electrical system that may take 1000's of dollars to track down. Of course, as a single mom, it appears that my lack of knowledge of car repairs, has disadvantages.
Does anyone have other possible remedies, suggestions, solutions?
Thank you for providing this site for those who are not mechanically inclined. :D