Does your fuel pump click for about 5 seconds EVERY time you turn the bike on? If the bowls are full, you should not hear the pump at all. There are multiple possible causes of this problem, but I wanted to post a solution that seems to be fairly common. I got some great advice when I asked about this issue, and here is how I fixed it:
The problem (for me at least) was a misplaced diaphragm in the fuel pump. You'll need to remove the fuel pump and take it apart to reinsert the diaphragm. Sounds a lot more difficult than it is. Start by removing the drivers seat and the faux tank. The next step is to remove the coolant reservoir. It comes out very easily - just remove the two hoses and slide it up:
Now we want to disconnect the power supply to the pump. Just follow its wire and undo the connector (there is a small tab to push on the underside):
Next you can slacken the two nuts holding the pump:
And remove the four frame bolts (take note of the three ground wires attached to the rear bolt on the right side):
Now you can compress the clips on the two fuel hoses attached to the pump, slide them down the hose, and remove the hoses from the pump.
You'll need to twist them a little a tug pretty hard.
Make sure you have a cloth underneath as a bit of fuel will leak.
Remove the nuts and washers from the frame and pull the fuel pump out.
Now remove the five screws from the same end of the pump that you took the hoses off and carefully take the top off. Be prepared for some more fuel to spill out, and look carefully for a flat rubber diaphragm about the same diameter as a pencil. You will have three sections: a 'lid', a center piece about a half inch thick, and the rest of the fuel pump body. Inspect everything. I had some rust-colored gunk that I cleaned up. The inside of the lid:
The middle section looks something like this:
Notice that there is a rubber tit sticking out of the top right hand hole, but nothing in the hole that the arrow is pointing to. The missing diaphragm in my pump fell out when I disassembled it, but you may need to look for yours. Here is what it looks like:
Place the diaphragm into the hole so that the tit sticks out where it is supposed to. I had to use a small screwdriver to get it in. It should look like this when you are done:
Thats it! Put er back together, start the bike, and then turn it on and off a couple of times. When the bowls are full, the pump should no longer engage and you won't hear the clicking. Oh yeah, make sure you put the pump back together correctly - When the lid sits on the body it should look like this:
Everything else is just in reverse. Good luck!