In general, fuses are placed between the power source and the load and any controls.
There are lots of exceptions of course.
An electric fuel pump has several controls. The ignition switch, the computer that lets run for a few seconds when the key is first turned on and then kills it if the engine does not start after a few seconds, and, of course, the kill switch which stops the fuel pump in case of an accident.
If I had to guess, the fuse is probably between the power source and the first control, which ever it it. Most fuse blocks have a power line direct from the battery for systems that need continuous power, a power line from the run position of the ignition switch, and a power line from the acc. side of the switch.
So, the pump fuse would then be powered by the run position. In that case, the short would have to be between the fuse and the ignition switch. Should be easier to find, since there is not as much area to search.
We still need a schematic though.
J.