A friend of mine drove a 2003 3.8L Mustang for 15 years. The only reason he stopped is because the ice in St Louis last week caused him to get into a relatively minor accident. Car wasn't worth fixing at its age. He drove it in high school and college, then took it to Baltimore and St Louis. They were decently made 'Stangs compared to nowadays. My and my girlfriend's 2017s constantly throw EVAP codes already. The 4.6L V8s are great engines, but they will be worn out, unless you find a low mileage one that lived in the garage as a toy. The 3.8L could be as well, if people drove like lunatics. Have a mechanic check one out if you're interested. 

Both the 3.8 V6 & 4.6 V8 feel a little under powered IMO by todays standards (190/260 hp respectively). Im not too sure about the reliability of the ford 3.8, but I believe the 4.6 was used in the crown vics, and they're extremely durable. Of course, all bets are off with a 23 year old mustang, who knows who was driving it before.

Can't speak to the V6, but I had a 99 GT, aside from being automatic, it was a good car, for what it was. At the time there wasn't a 5spd to be had for reasonable $$. Modern V6's have more HP than the 4.6L had, but then the car didn't weigh a whole lot, so it was more than adequate, especially if you didn't take it to the strip. And if you wanted/needed more power you could drop in a 5.4L or get a Cobra. Still see plenty of that vintage still driving around here in the southeast.