I've read back on the history of your problem here.
http://www.ukmonster.co.uk/monster/s...ad.php?t=57711
Seems like you've already had some good advice, and followed it.
As to the fuse blowing, my first thoughts would be a short, which could be hard to find and might even be hidden within the harness somewhere!! Prime suspect would be in that part of it that passes the steering head, where it flexes when the bars turn. You might be able to reproduce the fault by running the bike and moving the bars from side to side? Another vulnerable part of the harness is a "crook" more or less above the crankcase breather, just behind the vertical pot. Water can find it's way into the harness and pool at the bottom of the "crook" causing problems.. Sometimes.
Otherwise it's just a matter of carefully looking everywhere until you find it.. Not a great prospect!
As pointed out in the other thread, it could still be the fuel pump. This will draw more current if the filter is getting full as the load and therefor the resistance will build up. I can't think of any more obvious sources of resistance at the moment, but others might? You can do a resistance check on the pump with a meter.. StevieL would have the method and figures for that test.
You have fitted a new mosfet R/R. I can't emphasise enough, the need for good low resistance, weatherproof connections of the three yellow cables to the rectifier. I use Gold connectors on these, others hard wire, solder or crimp these cables. This won't be the cause of fuse blowing, but it is worthwhile checking the voltage at the battery terminals with the engine running to ensure that everything is working okay and there is not excessive voltage getting through. You should see a maximum of 14.5-15 volts. If you have a surge above that you might be lucky enough to blow the fuse before boiling the battery.
Finally. The missing phenomenon might be caused by dodgy connections to the injectors, which are fired electrically. The plugs can sometimes play up due to corrosion or wear making them loose. Mine looked perfectly normal but would not pass current from plug to socket! They only pass a signal current, so I doubt they would have anything to do with the fuse blowing, but worth checking thoroughly anyway.
This all sounds highly annoying, I hope you get to the bottom of it.