There's a problem with what you said.
The GSXR 750 used a 6 piston caliper from 1996-1999, and then used a 4 caliper piston from 2000 to 2003. The 6 piston and 4 piston calipers are not interchangeable. The GSXR 600 used 4 piston caliper from 1997-2000 and 2001-2003, but they were not interchangeable between the two sets of years. The calipers are interchangeable between the 1997-2000 GSXR 600 and 1996-1999 GSXR 750 and then between the 2001-2003 GSXR 600 and 2000-2003 GSXR 750.
So, as you can see, you can't run a 2001 GSXR fork with 6 piston GSXR caliper. So what, exactly, are you running on your bike?
Separately, the SV master cylinder should work with any of the conventional GSXR brakes, however, it's well worth upgrading to a conventional Brembo MC off a Ducati Supersport.