your 2006 bike was designed to run on 10% ethanol regular octane gas
if you are putting e85 in the tank... that might be a problem
is there any chance its an electrical problem, bad wire/ connector, corrorded ground connection, and when you replace the fuel pump the back connection sticks good for a while?
In a pinch you can bypass the fuel pump, and the bike will run with the tank from full to about half empty - you only need the fuel pump to get the last bottom half out of the tank, because the carbs are higher than the bottom of the tank.
Like Les said, after the first replacement I would have replaced all the fuel lines and filter, and pulled the tank petcock out to make sure its not plugged.