Yah flow 40's with longtubes and an h-pipe seems to be the best setup on the 99-04's. There are some other options ~ Pypes, Borla, Cherry Bomb (chambered ones) etc.
Chips are a thing of the past...handheld tuners are the way to go.
You can get an SCT tuner with custom tunes at American Muscle thru Bama Tunes and gain some power as well as be able to adjust parameters for gear/tire changes, rev limiters, etc.
You might pay more, $379, but you get free tunes for life, so it's a good deal.
12 Black GT500 SVT PP l 2.6 Pulley/Idler l Airaid l o/r X l 305 NT555R's l Recaros l
04 Azure Blue Mach 1 / 03 Sonic Blue 3.8 / 14 Sterling Grey F150 FX4 402A 5.0 / 11 GT500 R.I.P.