Has your car blown a head-gasket yet? If not and if you plan on keeping the car you should wait till it happens before you even touch the motor. Ford will repair it for free even if you no longer have a warranty.

I think you should trade it in on a 98 Cobra. You can pick one up for around $18k with very low mileage. It will be a damn nice car and pretty quick to boot. Or you could possibly find a nice used 99 GT for probably around $15-16k. If you wanted to stick with a V6 you could pick up a year old V6 too. Just make sure you get a manual tranny.