There is a rubber line that comes from near the fuel shut-off valve, and terminates at a connector attached to one of the cylinders, located behind the air-filter. The end of the hose, where it attach There is a rubber line that comes from near the fuel shut-off valve, and terminates at a connector attached to one of the cylinders, located behind the air-filter. The end of the hose, where it attached to this connector, is open. No plug, and I do not see any other hose that could have come loose.

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Hi, Rmarohn it may be a vacuum line that needs to be connected to the intake tract for this scenario you will need your service/owners manual if you can't find the first and best tool you ever bought for your Yamaha, despair not, for a mere $0 you can download another one. For more information about your issue and valuable "FREE" downloads that you will need please click on the links below. Good luck and have a nice day.
yamaha star 650 custom vacuum line diagram Google Search
Butterfly Vacuum Problem Part 2 Re routing vacuum lines
http://www.sloneservices.com/SilverBack/Other-Stuff/V-StarShopManual99-07.pdf
OEM parts for Yamaha
https://dd5394a0b8ca8e97ba29-abf76f3d91a2125517d6c7c409f095c7.ssl.cf1.rackcdn.com/content/common/manuals/1999/LIT-11626-12-30_126.pdf
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