I'm new to the GS and working on them, so please bear with me.
I just got my 850 running and have put about 200 miles on it. It has been running well for the first 150 miles, but began running rougher in the last 50 miles. Last night I was riding home and the engine stalled at a stop light. I got it started after a coupel of tries. The engine was running rougher. It felt like one or more cylinders were not firing at times. I made it home, but each time I would accellerate it would buck like it was missing. When I ran at about 3500 RPM it seemed fine, until I woudl accelerate again. When I pulled into the driveway it stalled after sounding like it was missing at least one cylinder.
All manifolds felt hot. I also have a sock for an air filter (I know I just got a new Uni and will put it in tonight)
So I am looking for a place to start. Air? Intake? Fuel? Plugs? What's your best guess

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