I used the 2006 Gixer brakes from a 750 - they were nearly new. All 600/750/1000 units are the same for the same model years. I believe you can use any since 2005. I did this right before the fix update was started.
The brakes are much firmer initially, but HiVel's updated stock brakes with the coated cylinders seem to work just fine. I never had issues like some others with the stock early brakes becoming mushy, but I liked the lever to be a bit firmer initially. The stock progressive system MAY actually allow for quicker stopping, but I have not had a chance to confirm or deny this with testing.