What year C4 are you talking about? They were made from 84'-96', BIG difference from the early years to the 96's . Regardless, yes an 03'-04' Cobra will kick the C4's a**, upside down and backwards any day of the week [yes even the ZR-1]
The 99' up Stangs are much more refined than the old 5.0's , smoother, quieter and faster. I still have my old 91' 5.0, they are a little rough around the edges compared to the newer Stangs but still very good cars, take a newer Stang for a test drive and if you like you're 5.0 then keep it.