About the best you can do, depending upon tire width, is to "bob" your stock fender, relocate the mounting struts to fit the Gsxr forks, and go that route. Else, you'll need a custom fender. This "fender issue" is the only downside to this swap in my opinion.
I don't like the look of the Gsxr fender on our bikes, and the stock is usually too narrow (120 tire) so a fiberglass or alloy custom is required. There are plenty of fender blanks available, you can then take some flat or round aluminum stock, heat it and shape it. Drill thru the fender and mount the strut over top from underneath the fender, and secure at the forks. Use 2 struts over the fender for a secure hold.
This is a stock front end, but the idea is the same: