Sprocket alignment has nothing to do with it, I'm afraid. The problem is clearance. I align my sprockets with a straight edge, front to rear and they are perfect. Every engine I've had has displayed chain interference at the place indicated in the link that maniac57 posted. Remove your clutch actuator cover and check. I'll be willing to bet that there will be evidence of the chain hitting the cover.I didn't have to do any grinding to run my #41 chain, if your sprocket alignment is good you shouldn't have any problems.
I disagree. I have no evidence of rubbing from my #41 chain. Chain alignment does play a role because if your chain is dog legging in or bowing out it is more likely to rub than if it is a straight shot from front to back... That is not only my opinion but has been my experience...Sprocket alignment has nothing to do with it, I'm afraid. The problem is clearance. I align my sprockets with a straight edge, front to rear and they are perfect. Every engine I've had has displayed chain interference at the place indicated in the link that maniac57 posted. Remove your clutch actuator cover and check. I'll be willing to bet that there will be evidence of the chain hitting the cover.
Tom