mods for 4.6
 

I recently purchased a '99 GT for a good price, even though it is an automatic it is a blast to drive. What I am wondering is where to begin on the upgrades? I knew where to start on my 5.0 but on this new car I have no idea. Only the basic exhaust, gears, and underdrive pulleys. If anybody can give me a clue I would appreciate it.

Well, your on the right track already. For the most part, the same starter mods still work.
* 3:73 or 4:10 gears
* H or X-pipe
* u/d Pulleys
* mufflers or catback
Leave your air silencer in though, as a number of people have seen losses w/o it. This is because Ford did their homework on designing it. It is a venturi/cone shape that by nature, flows more air then having nothing there would.
Since you have an Auto, you should most definately put on a tranny cooler. A plate style cooler is the most effiencent and you should put on the biggest that'll fit. I like the B&M 24,000 unit because its the biggest that still comes with an install kit. Heat causes 90% of transmission failure, so a $50 cooler is a no brainer. Ohh, and only use Merc V fluid also.
I highly recogmend getting a chip from www.customchip.com for your car. Their tuners know the 4R70W tranny better then anyone, and it'll improve your transmission fuction more then any other chip or dyno tune. Then of course, you'll have the benefit of bumped timing and other changes in the chip also. You can have them burn in a function so you can use a MAF from a Lightning, a piece thats as good as any aftermarket MAF for a fraction of the price.

RE: Air Silencer
 

QUOTE: Leave your air silencer in though, as a number of people have seen losses w/o it.

Are you positive about that? I took out my air silencer due to the advice of many of my fellow mustang owners (in case you couldn't guess, I have a 98 gt 5sp :) ) I've never heard that removing this piece decreases performance.

98gt: He's right about the hp losses. On basically a stock engine you might actually get a hp loss. MM&FF did an article about it last year in one of their issues and showed a loss of about 3 hp. That's really not much to worry about but it does happen on the 4.6 SOHC.