I'd consider the later MYs (03-04) if you can since Ford would have had a chance to iron out ****ling issues (e.g. TR3650 5-speed synchros) from the earlier years. In reality, though, the cars are all pretty reliable though being V8 Mustangs they might have led a tough life.
Consider checking the FAQ for tips and pointers for the 4.6 SN95s. You might also check for threads like this on buying used Mustangs:
Buying new Mustang, I need tips
I didn't immediately see one here but I'm sure it is.
A few things that immediately come to mind to be wary of:
- spark plug blowout: has it happened? how was it fixed?
- TR3650: is it clunky going into 2nd and 3rd? Was it fixed and if so by whom?
- car's modification history: did it spend the last 5 years with a 14-psi blower on it and has been returned to stock?
- rear gears: a common mod so listen for noises in the back and check for proper TractionLok operation
- front wheel bearings: seem to require more frequent than expected replacement so listen for noise from them at speed and when cornering
- engine noises: some piston slap when cold is normal but check for rod noises when hot as well as noise from the timing chains at the front of the engine
- Mach 460: 6-changer probably eats CDs...common problem
- fuel tank filler neck: gasket where it meets the tank can leak. check for evidence of leaks and/or fuel smell in this area
Of course there's the usual stuff you should check with any used car: maintenance history (oil changes especially), corrosion checks, suspension action (is the car lowered? if so, how does it handle bumps?), collision history, tire condition etc.