Fuse #14 60 Amp fuse in power distribution box ( under hood ) .
3 possible relays , more than likely only the two for the fans as the other one is for the PCM.
There is a separate relay for low speed fan and one for the high speed fan.
Here is a link to the wiring diagram for the cooling fans on this vehicle : http://www.freeautomechanic.com/98%20lincoln%20continental%20cooling%20fans.pdf
Without the manual it is difficult to locate as ford doesn't label the panel for some reason. You could test for power at each relay and remove the fuse ( fuse #14 60 Amp ) and see if you loose power, this should tell you which two relays are involved. They should be the same part number. Also, with a circuit protected power probe, you can apply power with the relay removed to see if the fan comes on( of course after suppling power straight to the fan motor to insure it works )
Example tool : http://www.powerprobe.com/