Problem with idling. Really killin me.

1984 700 So I tried taking my bike across Florida, but made it only 60 miles. I pulled off to get some gas, pulled in the clutch and was coasting to a stop, but I didn't realize that I would be legit coasting. The bike stalled when I pulled the clutch in. So I pull into the gas station and start it again. It starts rough and won't idle unless its choked. It will run off choke if I give it gas. Its running rougher though and with a whine coming from one of the front cylinders. I think i can rule out clogged pilot jets, being that I had taken the carbs off and cleaned my jets just last weekend. The only reason I bothered cleaning them was because I had to pull the carbs to change a leaking bowl gasket anyway, so I thought I'd clean the jets while I was at it. None of the jets were clogged though. I think It may be something valve related, but I have no experience with that so I'm asking the experts. Any ideas or tests I can do to diagnose my problem? Or anything I may be overlooking? Thanks, Nick

 

But did you make sure the pilot circuit is cleaned out? That's what usually plugs. How did you adjust the pilot screws? Did you sync the carbs once you put them back on? How good are the manifolds(boots)? Real hard, not soft?

What do you mean by "whine"? Is it a metallic tapping sound or more of a "whirl type" sound? The reason it may be running rough is your starting to foul the plugs depending how much choke your using to keep it running.

 

Whining noise is of deep concern from gen1. I would investigate that before moving on or riding further. Popping the valve cover off and inspecting is what I would suggest from this distance. Compression check would not be bad thing and could be quite telling.