Hello, I hope I can be of assistance.
You say the 40 amp fuse blows, is this fuse 21? If so I assume this is a 1997 to 2001 shape Mondeo, is this correct?
Let me know and I'll reply as soon as I'm able to.
Yes Fuse 21 yes 1997 to 2001
to start with try disconnecting both window switches to see if the fuse still blows, also try disconnecting the 1 touch relay that's in the drivers door, this way you can eliminate if the short is between the fuse box and either door or if it's in the door itself.
Check the wiring hasn't broken inside the rubber tubes from the car body to the doors as if broken it can short to earth. Below is the wiring diagram for the front windows to assist you.
I hope this helps but if I can assist further let me know and I'll reply as soon as I can.