would forks from a '03 600 gixxer bolt on my 99 GS?
Not without work.
You have to shorten the steering stem. And I doubt the stock GS wheel will fit.
I have a '99 gixxer 600 front end on my bike. Shortening the steering stem isn't enough - it's too thick for the GS neck. The gixxer stem is hollow aluminum, so even putting it on a lathe to take material off is not an option - there wouldn't be enough left. You could use your GS stem in the gixxer triple, but you need to make a press fit bushing to take up the slack at the bottom. I damaged my GS stem removing it (it was welded, not pressed), so I ended up having a machinist friend make me a new stem from scratch with the lower dimensions of the gixxer and the upper dimensions of the GS.
NONE of the stock GS components work with this swap. You'll need the gixxer fender, brakes, wheel, axle, master cylinder, etc. You will also have to convert to a bicycle style speedo or lose the speedo altogether because the gixxer axle is 3x as thick as the GS unit and the speedo drive won't work with it. The new gixxer doesn't use a traditional speedo drive. You'll also need to fabricate something to mount the headlight and gauges. All finished, it feels great and looks real nice - but it is a very expensive swap. Had I realized at the beginning how much it would eventually cost me, I would have stuck with an early 90's USD gixxer setup.