There's not really enough information there to make an educated guess. A loose (or worn) chain can effect shifts, but so can loose sprockets, or worn clutch components. When you indicate a "clunk" at a no-load shift (N to 1st), I think loose motor sprocket, or worse. If your shifter forks are worn, or you have a chipped dog or tooth, you can get clunking and grinding.
What year bike, how many miles, what condition is your clutch in? What does the chain look like? Have you pulled off the sprocket cover yet?