Do you have HH pads and SS lines? Bled-well? Then that is about it. Going from stock 1992 single piston calipers to twin-opposed (4-piston) calipers made a big difference to mine, but I also upgraded the fork from the 40 mm to the 1993+ 43 mm. That and switching to radial tires made the biggest changes in handling/braking. I also got Progressive Suspension rear shocks too.
I have adapters to take r1 calipers on wave rotors with xjr1300 master cylinder. But the brakes aren't great, better but not great. The feel of the lever is slight. Little bit like a mouse click, ideas?