I would start from your exhaust, better breathing makes for more HP. Maybe headers, Throttle body, mass air sensor. NOS is good but it does reduce the life of the engine(no offence to 1qwksvt). My 2000GT is a daily driver so I want to keep as close to stock as I can. A chip helps to a gaim of 6-10 % is common. Those combined should get you around 40 Bhp if done right. These are the plans for mine in the spring.
"I've been around long enough to know how ignorant I am. I don't assume the universe obeys my preconceptions. Hah! But I know a frelling fact when it hits me in the face." -Rygel
My ROUSH Rides
98 ROUSH Stage 2 GT
03 ROUSH Cobra
Or you could skip a lot of that and get new cams with a new exhaust. That should net you at least 50 hp.
__________________
Sometimes I think that government fits that old-fashioned definition of a baby: An alimentary canal with an appetite at one end and no sense of responsibility at the other.
- Ronald Reagan
50 horses is reasonable, whereas 100 hp can get expensive. I have been trying to figure out the same thing with my 98 Cobra.
I came to three conclusions after much research.
1) For about $1000, 50 HP is obtainable. However, for 100hp, you have to break into the piggy bank for around an extra $3-4K going N/A. And I decided that for the money, you might as well go SC and get a slam dunk 140hp for around $4500.
Getting the 50HP before supercharging and spending the first $1K is not a waste. My plan is: MAF, Cat-Back, CAI, UD Pulleys, plugs and wires (ie good old fashion tuneup), and a dyno tuned chip. All of which will help when you go SC, except you will need a new dyno tune and plugs.
2) I learned it is not all about HP. It's about performance and acceleration. So, gears, DR, short shifter, etc... although don't add any HP on paper, they make a huge difference in how the car pulls and performs. maybe more so then more HP alone.
3) 4.6L is expensive to make serious power, as compared to the 5.0.
Hope this helps
__________________
-1998 Black Cobra, Kenne Bell 2.1L Supercharged
-2005 Mustang GT, Premium, 5spd, Redfire, Mac Catback
-2007 Roush Nitemare Stage 3 Supercharged #48 of 100
Heads, cams,exhaust,Intake system,I wouldnt stick NOS on a stock bottom end of a 99, forge it first,been there, done that,, Oh !ya, Had a LS1, and a LT1(LPE vette),and the 32 v motor makes more power band HP, trust me. , All depends how deep ya pockets are Lad.Have fun!
__________________
99 Cobra 20K miles
Kenny Brown modified ( at there facility)
Full Sub system
Eibach Pro Kit
SHM Stage 2 heads
SHM stage 2 Billet cams
SHM Modified Intake
Steeda timing adjuster
Caster/Camber
FR headers
Bassani X-pipe W/cats
Bassani cat back
FR 4:10 gears
Full IRS suspension mods
T-45 modified(synchros and stuff)
Steeda TriAx shifter
WMS CAI with 95 mm Pro M
Original Cobra R wheels 17"
Nitto NT 555 Extreme ZR's(275 back, 255 front)
Autometer shift Light
Wake up my 1999 Cobra 
, All depends how deep ya pockets are Lad.Have fun! 
