If the fuse hasn't blown then it isn't likely to be a short circuit. More likely cause is poor connections between the plug and the relay. Did you clean all of the tarnish and burn marks from the wires before bypassing? Poor connections generate heat as current jumps the gap. The hotter it gets, the less current that gets to the load (the fuel pump) and the worse the damaged gets and so on to the point where all the available power goes as heat, then opens the circuit permanently or causes a fire.that would have melted the plastic connection where it plugs to. right?
If you can remove the female lugs from their plug, either replace them with new lugs or, as I've done in the past, squeeze them carefully with a pair of pliers. The first time I did that, I needed a pair of multi grip pliers to close the plugs together when I'd finished. I ride that bike another 100,000km without any further electrical gremlins.I´m waiting for one to arrive but afraid it will happen again. Gonna look at all the connections on the fuel circuit as you said before. the old one literally started smoking, i also bought a fuel pump and noticed that the plastic connections from male to female are a bit on the loose side. i´ve seen somewhere that to solve this we should twist the male plugs little bit to one side.