I have heard the 99+ stuff is better, but that I'm not sure.
I run stock 94/94 stuff on mine with no issues.
In terms of GT/V6 front brakes, then yes, 99-04 10.8 front brakes are better than 94-98 GT/V6 10.8" front brakes.
But the Cobra/Bullitt/Mach 1 13" brakes are better than both of them.