I just upgraded my suspension on my 03 GT this past weekend with Roush lowering springs, shocks, struts, and CC Plates. My question is how rough is the car supposed to ride? I mean I expected a slightly rougher ride with the stiffer suspension but I'm bouncing around like I'm inside a popcorn machine. Is this normal? Do all authentic Roush Stage 3's ride like this?

you dont see the benefits?.... reduce body roll/more control through turns/ increased responsiveness and of course looks... to name a few.
Assuming that all the parts you put on the car were in good working condition and that everything was installed (stock or aftermarket isolators and bushings), you're just experiencing what it feels like to drive a lowered ford!
But for some strange reason the back dropped lower than the front.