One of the first things you'll notice about a Ducati is how awesome the brakes are when you first ride it. Now, try and haul your speed down from 90 to 40 mph as you're running into a turn too hot and they are absolute shite! Read below about my learning curve with Doo-cah-tee brakes.
Note that I have found that the 2000 M900ie brakes to be superb as delivered. Asking around in the industry, I've learned that people believe the newer "twin pin" calipers fitted to `98 and newer Ducatis to be stiffer than the older, single pin ones.
EBC FA-95HH Brake Pads WOW! These pads rule... They have great linear feel, coming on light initially with very extreme ultimate power. They do get a bit hot... they roasted my DOT4 brake fluid, forcing me to switch to DOT5. They also don't lay dust down on the wheels.
Pads summary: Galfer Green pads, hella expensive, extremely high initial bite (too high for the street), great ultimate stopping power, much dust. EBC Green Stuff's: Better initial bite (softer) than the Galfers, but more than the HH's, too much dust. EBC HH pads are strongly recommended for stainless steel rotors on all non-SP Ducatis! I later discovered that Ferodo pads are the best for cast iron rotors on the SPs and from aftermarket kits.
Braided brake lines are good, much better than stock. The Earl's look hokey when next to the nicely finished Goodrich or Galfer lines. The thing to do is shorten one of the lines so it would wrap over the fender between the calipers. The fittings also look pretty good.
Note in the pic to the right that I run a single line from the master cylinder to the right caliper (where the stock double banjo bolt from the master cylinder now is) and then run the second line over the fender to the left caliper. This really cleans up the cockpit. The arrows point to the double banjo on the right caliper, the safety wire securing the brake pad retaining pin, and the faux Race Tech suspension on the shop cart.
Braided hose summary They're all good. Get hoses that have heat shrink coating so they won't saw through things. I like the single hose from the master cylinder to minimize clutter. There are kevlar lines on the market. They're OK, too.
Nissin ZX7R/CBR900 Master Cylinder. I got kinda pissed when a few hot laps up and down Palomar Mountain rendered my brakes nearly useless, so I threw on the ZX7R master clyinder from a `97 model with 6 piston calipers. Almost no lever travel and insane braking power. I'm happy. The Kawi remote reservoir unit does not come with a reservoir mount, so I mounted the reservoir to the top pinch bolt of the master cyl, using a longer bolt and a collar to space the reservoir off the mounting clamp. It works and doesn't look corny. Or get a CBR900RR master cylinder as it has its own support for the reservoir. This, too uses a 10x1.25 pitch banjo bolt as opposed to the stock Brembo/Ducati 10x1.0.
Nissin master cylinders that are similar to the CBR900RR one are available from Cycleworks for $159. Read about the kit. Banjo: 10x1.25