No special tool is need to service the fuel filter. I've had 3 EFI mustangs and changed teh filter on all of them (a couple times) without any special tool.
I run full synthetic oil so I go a bit more than 3K miles. The other stuff I would do at about 50K miles. And yes even the diff fluid. When it gets old, black n nasty bad things happen. My 00 is at 68K miles. Wuzz a little over 40K when I got it July 04. I want this thing to hit 200K miles so I will take care of it. Now I need to go pick up a ford fuel line tool.
make sure you get the 5/16" tool. mine cost $10, its made of aluminum. here's a how to. this site has a lot of good how-to's for general maintanance and performance mods as well. its bullitt specific, but pretty much the same on 99-04's, especially on 02 and up.