You say if you pinch off a the fuel line then the bike runs on both cylinders. Leading me to think you have a faulty fuel petcock. The diaphram in the petcock could be bad and is pouring gas through the vacume line causing that cylinder to flood. When you pinch off that line it gets less gas through the vacume line and therefor starts to run.
Let me know which cylinder you pinched off. There should be three lines to the carbs. A vacume to the inside front of the left carb and a fuel line to the outside rear of the same. And a fuel line to the inside rear of the right carb.
Let me know.