The Dunlop brakes, in my view are a bonus from all regards. The back brakes are much easier to fix than the later Girlings, even if they probably need doing nearly as often! Brake rotors, or discs, are actually easier to source than for Girling cars. Seal kits for the fronts are easy, (common with early JAguar E type) but I have a feeling the rears may be more difficult as they are an unusual size. The rear cylinders can easily be replaced with the next size up, though, which is a Jaguar standard. For the same reason, new cylinders for the front are easy. My only concern would be if you have a Dunlop booster, or servo. I don't know what the availability of parts for these are, but I have a feeling... But then, Rover used the later Laycock/Girling servo with the Dunlop wheel set up, so no reason why you shouldn't do the same! Your car is right on the changeover to the Lockheed/Girling master cylinder and servo so it could have either.
The holy grail 2000 braking system is the Locheed/Girling master cylinder and servo with the Dunlop wheel cylinders etc. This stops the best of all the 2000 set ups. The other alternative being to fit the front brakes from the 3500 (which are Girling 3 pot calipers common with the later E type) which should improve things slightly again. On my 3500 (Lucky) I have these 3 pot calipers split and spaced out to take vented discs, microgrooved with GreenStuff Kevlar pads and a set of Dunlop rear brakes ready to go on to replace the Girling set up. The backs will be fitted with the next size up cylinders and again microgrooved discs and GreenStuff Kevlar pads.
Chris