Another problem that can cause wierd fueling issues is a blocked breather from the tank filler. It will cause the bike to splutter or conk out after a short ride, start again after a little while, and then conk again once you get going. Squirt a bit of WD40 into the breather tube and gently blow some low pressure compressed air into the tube, and watch for a dribble of WD40 out the bottom. This will confirm that it's not blocked, thus eliminating one potential cause.