I'd personally start with making sure the forks were straight in the yokes. T o do this: you'll need to support front of bike with either a front paddock stand that attaches under the bottom yoke or you can, carefully, use a block of wood under the sump and jack it up with a trolley jack / car jack. Then loosen off all the retaining bolts on upper and lower yokes (if you haven't supported bike at this stage, it's gonna fall flat on it's nose!!!) and loosen off clip-ons too. Then stand facing bike with front wheel between your legs and twist it all straight. SIMPLE! Tighten it all up again and re-check your throttle distance compared to other side.
If it's still un-equal, you'll have to whip off your throttle, front brake and switch gear to look at clip-on more closely. If it's obviously / badly bent i'd just suck it up and buy a new / replacement one. If it's not TOO bad you may be able to GENTLY straighten it.
Hope that helps!
By the way, i'm no mechanic so you might want to enlist the help of someone more qualified than me for advice!!!!!
If it helps put your mind at rest though, when i had my G2 ZX6R, i binned it at Cadwell Park, (DON'T ASK!) and i had to do all the above too. I ended up having to buy a replacement clip-on. Got a pair off ebay for a tenner. BARGAIN!