I haven't got any powerflex stuff on my GT, but I do have Koni FSD and Eibach springs and I can tell you it doesn't equal anywhere near a harsh ride, i wouldn't keep it if it did. Mine was remapped before I bought it, but the brakes really ought to be better for the amount of power and weight on tap. I'd do your brakes first even though the thought might not seem as gratifying as a remap or dampers. Make sure you've some nice tyres too, they can alter the feel of the ride massively.
GT 3.2 V6 - Q2, KONI FSD & EIBACH PROKIT, GTA REMAP, MICHELLIN PS3's, BMC CDA
159 SW 2.4JTDM TI - ALFATUNED, WIZARD BACK BOXES, KW V3 COILOVERS, NOKIAN WR A3/MICHELLIN PS3, PCA DYNAMICS ALIGNMENT.