I have the FE 450, so I don't know whether the wiring's exactly the same but I've had a look at the manual and the fuel pump wiring does look the same as far as I can see. I had various problems with the pump, though it never actually blew the fuse so yours may be something different, but FWIW...
The pump failed and left me stranded. It was definitely the pump itself as there was power at the plug but the pump didn't run. This didn't blow the fuse but there must be a chance that it could if the pump was seized or shorting internally, so even though you have a relatively new pump there is a chance the pump itself could be the problem.
After I had the pump replaced, it ran ok for a couple of hours then stopped and left me stranded again on the next ride. This time there was no power to the pump. Turns out that when the subframe was off to replace the pump it had disturbed the wiring loom and the power to the pump was going through a joint that was badly corroded, and it actually came apart and the two bits were just resting together and eventually moved and lost contact.
The joint that failed has 3 white-red wires joined together. 1 comes back from the voltage regulator (near the headstock), 1 from the power relay and the other from the fuel pump fuse, and the joint's buried deep in the loom where it comes down from the battery area between the tank and the subframe, just aft of the point where it passes the vertical part of the frame (so it's right alongside the rear shock). It was corroded so bad the wires just fell apart, but the joint was still covered in heatshrink sleeving (probably the only thing that kept it together this long) so it was in no danger of shorting on anything and in any case it's upstream of the fuel pump fuse so it wouldn't blow that. If anything, the main fuse would go so it doesn't seem likely you have the exact same fault.
Your fault is likely to be in one of the following places:
* In the fuse box somewhere near Fuse 2 (fuel pump).
* On the black-blue wire between Fuse 2 (fuel pump) and pin 14 of the ECU.
* Inside the ECU (i.e. the electronics have failed).
* On the blue-green wire between pin 15 of the ECU and the fuel pump plug. NB: The book says this is blue-green on both the FE and FX, but it's white-blue on my FE. Easy enough to check as you can see it where it goes into the plug at the fuel pump.
* A short in the fuel pump itself.
I'd take out the fuel pump fuse and unplug the ECU and the fuel pump so you can test for a short to ground on each section of wire in turn, wiggling the wires around while you test as it sounds like this is an intermittent problem so it may only be there when the wire's in one position.
If you can't find a problem on the wires, test the resistance of the pump. Should be 1.0 to 1.8 ohms at 20C/68F. Even if that's ok it doesn't guarantee the pump's not faulty as it could be jamming up when it tries to turn which would draw more current on load, but you'd need something like a clamp meter to check that.
If everything else looks ok it could be the ECU but that would be tricky to test as the short might only be there when it's powered up which means having it plugged into the bike and that makes it hard to isolate so you're just testing the ECU as you can't get at the pins without a specialised test harness. Easiest way might be to borrow another ECU and see if it solves the problem.
Good luck!