Personally, its your call but I'll give my .02 cents and say stick with the automatic. Go to
www.tccoa.com and look up the articles for the 4r70w automatic transmission. It can be modified to handle some serious power output. My advice is the following.
Transmission cooler - A must have for any auto tranny as heat is the number one killer of the automatic transmission.
Shift kit - Ditch the transgo and do the "Jerry mod shift kit" or get a new performance vavle body from some place like Lentech transmissions or Performance automatic. You'll be glad you did in the long run.
Torque converter - You're already going to spending some serious money to rebuild the automatic and while it's out of the car, you might as well get a high stall converter to put back in there rather than the stock one. I recommend a Precision Industries Stallion series converter with no less than a 2800 stall. Anything less than this would be a waste. I got my torque converter from
www.houstonperformance.com shipped to my door for 714 dollars. Expensive, yes it is. However, you can get it installed when you get the transmission rebuilt because to rebuild the tranny, they're going to have to pull it from the car and when they pull the tranny, the torque converter comes out as well.
Gears - I suggest at LEAST a 3.73 gear ratio. I would say no less than 4.10's but you do have a 98 GT with the Pre PI cylinder heads and cams found on the 99+ models, therefore, you don't have as much of a powerband. 3.73's would be good, but 4.10's would be awesome. You can get gears for pretty cheap at
www.mustangtuning.com or from Randy Stinchcomb at Liberty Ford. You can contact him over at
www.modulardepot.com He can also help you out with getting some of the Ford parts you need to rebuild your transmission.
If you have any questions, feel free to ask and let us know.