One thing I can think of that would cause intermittent problems like you describe is variations in the quality of the fuel. Are you getting the fuel from the same station each time? I imagine you don't , I know I don't always get my fuel from the same source. I would make a note of the location of your fuel purchase and how the bike seems to be running to try and see if there is any link to a particular petrol station or brand of fuel, here in the states I have a few places I won't buy fuel from if I can avoid it and I also have a few favorites such as Mobil or Shell branded locations.
Another thing you might consider is if the fuel filter has ever been serviced? There has been issues with the plastic fuel line inside the tanks developing small pin holes in them which can cause drivability issues. From what I've read on the problem the bike will run fine when the tank is full, but as the tank level gets lower exposing the pin hole/holes the line will draw in air, starving the bike of fuel.
I change my fuel filter and inspect the lines inside the tank about every 20,000 miles, it only takes about one pint of beer's worth of time to get it done.