Two things will cause your problem. Chain too loose or misalignment.
How tight is your chain? You'll want to have 1/2" to 3/4" slack in the chain. To measure this slack leave the clutch engaged and roll the bike forward until the piston goes into the compression stroke. The top chain run will then go slack. That's where you measure the chain tension.
If the chain is being pulled off to either side due to misalignment with the rear sprocket that can also cause the chain to run against the engine case.
The master link snap retainer should be installed so the closed end enters the engine sprocket as the bike moves forward. Having the open end first can cause it to snag and be popped off insude the clutch actuator cover.
There should be no need to grind the cover where you indicate the chain is hitting.
There usually is chain interfernece inside the cover. There is a thread on that that I'll post a link to. http://motorbicycling.com/showthread...newpost&t=6682