My experience of SS rear brakes on mates bikes was that they all worked, and they all stuck on at some point creating various levels of fire!
Stock brakes in good nick work fine. Imho, no need for upgrades, just fettling. +1 for EBC HH My 2003 999 doesn't have radial but works just fine. Like the look of radial calipers though and those rather nice disc locks fit.
Have you looked to see if the discs are vertical to the calipers. If they aren't and you've got floating discs the you can bleed all day and it will feel spongey. When I fittted a new caliper to my 750ss I had to shim with stainless washers to even up