With a 2000 model,you already got tha P.I. improvment.So time to hit the aftermarket.Trickflow now makes heads for the 4.6,modularmustangracing.com offers these heads in 3 stages of porting,livernois offers factory heads in 3 stages of porting.several companies offer cam kits and intake manifolds.The bolt-on options are endless.
I've got an '02,so we got the same powertrain.The main thing i feel needs to be addressed before upgrading is that weak,funky tremec 3650 5speed,giving your car is a manual.I'm eyeballing M.M.R.'s protrans 750,which is a TKO 500 worked over by MMR,said to handle up to 750hp or 10.00sec car.I dunno how well tha autos are holding up.My suggestion is definitely consider how you intend to drive the car and power level you wanna run,then research your transmission's performance under these guidelines,I,m sure guys in here could tell you about any trans options you could think of.
I can tell you all about tha trials and tribulations of a stock 3650 in a car with 3.55 gears(stock other than that)and the quest to achieve the quickest(not power-shifted)shift.