Favorite year: 99-00 or 01-04?

I say '02+ for sure.'01's are mixed matched,the in between year.....maybe romeo,maybe windsor,maybe t45,maybe 3650,maybe plastic coolant passage on intake,or maybe aluminum coolant passage LOL
The '04 year should be the best of the bunch,and improved with those concerning issues like with the 3650,the cylinder head tick,and sparkplug thread issue.
 
I always liked the 04gt spoiler the best. I think it looks alot better but everyone has a preference I guess. Honestly I would go with a low mileage 04 but if I were you I would definitely look around for a Mach. I've seen one go for as low as $12000. I can understand your desire for upgrading a gt but you can still do alot with a Mach and you'll have a better performing motor and suspension to start with.
 
The newest car you can afford is always the right answer, but either way the '01-'04 would get my vote. The Romeo engine seems to get all the attention with the aftermarket since that what most Ford 2V's were running. The Windsors only got a short 2-year run in the Mustang and was otherwise designated to Truck duty.

Mechanically, one is really no better than the other so at this point you're pretty much addressing age and wear and tear.