Be careful what you wish for, I started down the brake upgrade route with 'just' a radial master cylinder but then got a little carried away; Must learn some restraint! Bloody good brakes though...
As Andy said they should be fine, stick some decent sintered pads in, I use either Brembo or Ferodo's, if you need more grab and stopping power you'll need to go down the master cylinder & iron disc route. As Tim says though it's easy to get carried away
I upgraded the brakes on my 996 to the brembo p4 ones the other year. That and new fluid/pads made a world of difference. Those brembos came on a variety of bikes, such as aprillas and ktm superdukes and so dont just search for the ducati ones which tend to make more money. I think I paid £130 for my set, but they tend to go for between £150 and £200. They bolt straight on, although I also took the opportunity to replace the hoses with the 748R setup whilst I was at it. All bolt on stuff.
Axis make the rotors...usually to order for older ducatis. Ferodo sintered pads are fine.. .you can source the rotors suppliers easily but i had to wait about 3 months for them to do a run of ducati 996 rotors...thats my 2 cents worth....but gees theyre wirth it. Sent from my SM-G925I using Tapatalk
I bought a set of Moto Corse radial fork bottoms for the standard Showa forks on my Y2000 748R, and then a set of monoblock calipers from fleabay, it was awesome