The main difference in 94-98 and 99-04 3.8 engines is that the newer ones have a split port intake/head setup. There are other minor differences, but basically the heads and intake account for most of the 40 extra hp.
Doing a "split port swap" is a common thing for single port owners. Do a search on this over at www.3.8mustang.com
. They have enough over there that'll make you an expert on this little essex engine.
2002 Mineral grey GT 5 speed. Flowmaster 40's catback, Mach 1 grille delete, timing advance, push button starter, Bullitt pedals, FR500 steering wheel, K&N FIPK, Self ported upper intake w/ spacer, Pioneer Avic D3, MGW shifter, MM FL subframe connectors, Mach 1 springs, Bilstein HD struts/springs