Starting late last year my 1996 CBR600 F3 would develop a knocking noise in the engine on the left side when it was ridden over an hour on a warm day and I was going along at low RPMs. The bike didn't appear to be overheating.

The first thing I tried was a gas additive that would clean anything out if there was any carbon build up.

Next, I adjusted the fuel-air mixture screw so it wouldn't run as lean in the hope that would help. Still had the knock.

The knocking does not happen when idling or when I have the clutch level pulled in.

Does anyone have ideas or suggestions?

 

Have you tried new plugs?
Check the oil level. Maybe an exhaust leak too.
Try adding some Marvel Mystery Oil.

 

Damn. It sounnds like you might have rod knock.

 

You said it doesnt do it with the clutch pulled in.
Maybe something to do with your clutch?
I dont have much experience but sounds like a first step to look at to me.