This happened to a friend of mine with a 99 Cougar. He took it to the dealer and they told him that there were some bad flywheeles cast for the 2.5 in 99(they said about 1 out of every 100
), and that 1-3 teeth were missing from the flywheel
. They had to pull the motor out to replace it it took a week,
at least it was covered under warranty. BTW, when this happened this car was less than 3 months old. Sounds like there was some bad casting that was not caught at ford. All I can say is that I cant imagine how it got past production/installation like this (I saw it after they pulled it out).
I am afraid this is bad news for you. I suggest you try to live with it, because sounds like you will have to pull the motor to fix it.