One way is to go back to where you found the #41 master link and buy a length of chain that will fit your installation. #41 is interchangable with the kit supplied #415 as far as sprockets go but there is enough difference that the master links are not interchangable. That's why it bound up in the clutch/sprocket cover. The #41 is probably a better chain anyway and will work for you. Good luck.
While we're on the subject there is some interference with the chain and clutch actuator cover on almost every kit. I'll look and post a link later for you on that modification that will eliminate some chain noise.
Try this> http://motorbicycling.com/f4/chain-noise-6682.html