Legally, if he's under 18, his parents have a LOT to do with selling the car.
I'm pretty sure there are just as many parts for the 2001 as the 2005.
That being said, I'd stick with what you have for now. $9K for a stock GT is over priced...even with the low miles. If you really want a 99-04 GT, shop around more. There are FAR better deals to be had.
The other thing you should look at is seeing the V6 and the auto as a bad thing. The V6 is a stout motor - not 'paper thin'. An auto isn't a bad thing at all for a street car. If it were a pure track car, then I'd say match the tranny to the type of racing. Being that you're young (guessing), take your time and learn about the car you have. Drive it to it's fully potential prior to 'needing' to jump to the 5 sp V8.
1998 Roush: M112'd Aluminum block 4.6L 2V 6 speed track car
1999 SVT: Mostly stockish
1970 Mach 1: Resto-modded monster
2000 Roush #5004 - World's FIRST M112'd V6 Mustang. Sold, but not forgotten.