I, and many others have used half links with the cotter pin and never had problems. Which side are you putting the cotter pin on? Inside or outside of the chain? In other words, is the cotter pin facing the engine when it is at the engine drive sprocket, or away from it?
There is an old thread here about grinding the clutch actuator cover to eliminate chain interference. Maybe that's what you need to do.
You'll need to look for where the cotter pin is hitting and grind away that area, if not too deep.
Tom