Other than the axles, everything is cosmetic. If you want to go aftermarket with the radio, the '99 is way easier. The big double din box of the '01 is a pain. Very few adapters and aftermarket stuff that is decent without modifications. You will need a schematic to get the Mach 460 hooked up right with the non-factory stuff to work properly. There is plenty of aftermarket stuff to plug right into the '99 with no issues.
As for the seats, you can go out and get Sparco or Recaro for a good price.
No Cobra on the bumper? Big deal. In my own opinion, I would rather see no letters at all as it looks cleaner. Every time I see those highlighted letters, it reminds me of those Cutlass SX's with the big letters across the bumper.
Smoked headlights? It depends on the color of the car. Vibrant colors, like Rio Red, look better with the clears. If you buy the '99 and want smoked, go to a junk yard and take them off a late model 'Stang.
Looking at it from my perspective, I would get the '01. Ten K less miles, two years younger, depending on the build date, and it probably has some factory warranty left. I like the '99s myself due to the fact that I drove one (Rio Red 'vert #3684. I wish I had it back.) until I got my '03. Dollar for dollar, though, the '01 is a better buy unless you intend to do a lot of mods right away.
Good luck!
