It is probably the resistor. I had the same problem with my 99 Cougar. It is located on the passenger side under dash. Check with Ford. I think that this part was recalled.
I had the same problem with the same year car. I've replaced the resistor several times. It works for months & then it stops working again. I think this is the 4th time I replaced the resistor, it is working okay now. I think it is a defect in with this cars fan system. I had a similar problem with my 2001 Sebring Convertible. I had the blower motor replaced, and now the fan works perfectly.
One common problem is the resistor, they like to get to hot and melt. The resistor is located under the passenger side glove compartment, by the fan motor. There should be two screws holding the resistor in place. Unscrew the resistor then unplug it from the wire harness. If it looks burnt or is melted, then chances are this is the problem. Plug in the new resistor and screw it back in place. It is a cheap fix and is easily accomplished.
More than likely the culprit is a defective blower motor resistor pack. It can be the switch itself, but it is unlikely. I replaced the switch and had the same problem, its most likely the resister, this is a recall so your local ford dealer should fix it for free if not id call up ford and complain
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