well the 99 up v6's are DEFINATLY faster than the pre 99's stock and you woudl be very wise to stick with 99 up, however the 99-00 have pcv issues and to much oil can get into the upper and cause detonation (pinging noise may not be noticable or able to hear until high in the rpms) the 01's up fixed this so it might be wise to get an 01 up mustang its only a little more.... 01's with manual tranny (only way to go) will run you 9k-10k~ in good to great shape. other than the PCV issue and some have gear whine noise noticable when you let off the gas at a given mph and coast, so speed up to 70-80 and just coast down with the windows rolled up all quiet if you hear a whine in the rear its the gears, if you dont then your good now worries, its not somethign thats gonna break on the car, easliy fixed its just an annoyance nothing more. thats the only issues to look out for.
if its a manual listen in the back of the motor area, tranny shifter area inside the car at idle for a ticking noise with the clutch out, might have to shift alot and use the cltuch alot and get it warm to notice, if it does its a throw out bearing, cheap easy replace able part, 200 buck max, also get the clutch replaced if miles are high cheap also. make sure all gears shift smooth (the T-5 is a notchy tranny so it wotn be smooth... just listen for grinding, especially shifting into 5th and second.