Hi Auburn,
Before any parts are blamed, are you sure your calipers are fresh? How long since a rebuild? How about the master? If those are good, proper and thorough bleeding can't be over stressed. A banjo bolt with a bleeder at the master really helps, as well as starting with the caliper pistons fully bottomed in. Also, even holding the calipers with the bleeder at the most upward position and also tapping on the caliper, lines, and master to get air bubbles moving upwards toward the bleed valve. Once the system has been gone thru with the pistons full in, pump the master until pressure builds up (pads on rotor), hold lever and open the master bleed valve under lever pressure, close bleeder when lever bottoms. Do that with calipers too, working top to bottom. Obviously keep doing the above until there is not even a hint of air coming out. You're there when the lever feel feels firm right away, with minimum lever travel and pressure. Sorry if that was all too basic.
Brembo masters should have the piston size stamped (not a cast number) on the bottom of the body. I've always used the Vintage Brake chart to size a master to the calipers with very good results when shooting for his "sweet spot" range. With two F08 calipers (four 38mm pistons) that spot would want a 14mm or 15mm master piston, like this one
http://www.yoyodyneti.com/ProductInfo.aspx?productid=10.4620.67. Brembo parts are just fine, as long as all the components are properly matched up. Ducati may have been a little sketchy about this back in the day. Fresh clean pads designed for how you will use your bike (street or race) and rotor material (stainless or iron), and rotors scrubbed clean with brake cleaner and Scotch-Brite, then the pads properly bedded in, should give you the results your looking for. I love good strong easy to modulate brakes.
Bill
