Hello,
I was wondering if you got the front brakes completed. I have a 97 RS and had the front rotors replaced and bothe calipers rebuilt. When I got the bike back it felt like the front brakes were a little spongy. I called back to the Yamaha service center and they said it could be some air in the system. They said they sometimes will tape the brake lever filly back to keep pressure on the system and let it at least overnight. I just untaped it and it felt much better.
Just wanted to let you know of a quick and easy routine that might cure spongy brakes.