Answers please

Those "tune-up" places aren't worth it unless you have no idea how to turn a wrench IMHO. In addition to these tune-up shops, the dealerships also charge a hefty price for such "rountine tune-ups."

Also, your 99 has a Coil-On-Plug (COP) ignition, so there are no old-school sparkplug wires per se, if you take a glance under the hood. Changing the plugs on these engines is very easy to do (make sure the engine is completely cold though, because of the aluminum!). Just remove the spark plug cover plate on the top of the valve cover and you will have access to the coils & the sparkplugs...it's very straightforward.

A lot of folks will run Autolite copper plugs - copper won't last as long as the factory platinum plugs though. Many racers prefer using a copper plug and they are relatively are fairly inexpensive, so changing them more often than a "100,000 mile platinum plug" is no big deal.
Other popular sparkplug choices are Motorcraft, Denso Iridiums, NGK, etc. Be warned though, some of the sparkplugs out there cost a pretty penny.
Changing the oil yourself is probably one of the more easier tasks as well - save your money & perform the tune-up yourself. While you're at it, you could change the fuel filter too - at 50K miles, it's probably a good idea.

The following websites are great resources, Joe Lynch & Shane's (TXSnakecharmer) pages. I suggest you bookmark them and take the time to read through them. You will find plenty of info & lots of "how-tos" on how to work on your '99:

http://www.lx.net/jlynch/

http://www.shane.roberts.net/cobra.htm

G'luck!

if your somewhat mechanically inclined you can do all the tune up work yourself. Motorcraft plugs are my choice if your running natural, msd or motorsport plug wires change your PCV valve, definetly change your fuel filter and if you have turned 50k i strongly recommend that your have a total fuel system flush. It doent cost all that much and you can feel a difference.

just change the plugs that's all you need

Just change the plugs, My 01 Cobra has 17,000 mile, no need for a tune-up, got a wild hair and picked up the Denso Iriduim plugs, 15 min later I had a completely diffferent car.

I say if you can use a screw driver and a wrench, you can do just about any mainteneance item to your stang, save the money you would pay someone else for mods.
Plus it will give you a more personal feel for you ride.

Tune ups are easy. Make sure you change your points, they are always a good idea. Get a good carb. rebuild kit, makes a world of difference. New fan belts aren't a bad idea either.... oh, wait.... that was for my 65.....lol....