Blown fuse
 

I have a 2001 Grand Marquis. Starts and runs fine, after running for 45min to 1 hr it blows the #2 fuse under the hood and battery is dead. Owners manual says it goes to the generator/starter relay. If I change the fuse immediately it blows when I try to start the car. If I let it sit while I charge the battery it will start up with no issues. The alternator is putting out 13v, it has a new starter. and battery is new. I swapped as well as tested relays and have a new set on order to replace all of them due to age. I know I have a broken wire in the drivers door harness due to loosing power to driver side windows but have not traced that issue down yet and don't see it as being the issue. Any suggestions on where to start looking to correct my blown fuse issue???

Even though you have a suspicion about the driver's door harness, it's worth checking all wiring and connections in the vicinity of the starter relay and generator. Look for any signs of fraying, damage, or corrosion. Pay close attention to areas where wiring might come into contact with metal components or other wires.