You cannot go wrong with a good set of quality struts and shocks (i.e., Bilstein, Tokicos, Ford Racing, Yellow Koni, etc.) Don't forget to upgrade with GT500 upper strut mounts, bump stops and some camber bolts (depends on alignment specs).
Personally, I currently have those same Ford Racing Struts (listed above) with GT500 track-pack rear Bilstein's & Ford Racing "P" springs (1" drop) on my 05" GT, car handles like it's on rails but stiff... I also have F/R big sway bars and all sorts of braces.
FYI I had F/R Tokiko's on my old 06' GT Convertible with adjustable on the rear with GT500 springs. Loved the way they rode and handled very well.