This may not be the case but check the spark plug wires themselves. I have an eclipse that had the same problem you describe. I could not for the life of me figure out what was wroung. Everyone I talked to said to check/replace something else. Check the spark plugs, check the exaust.... no one ever said check the wires... I finally checked the wires for some reason and one of them was shot. Replaced them and instantly it was like driving a new car. And it only cost like $30 for a set with a lifetime warranty.

-Greg