I know they make one for the 4.0 and the 3.8, not sure if the 3.8 will work on the 3.9.
Can't find anything yet for the 3.9.
Procharger has one here for the 3.8. Read up.
Intercooled ProCharger® Systems
for 1994-2001 3.8L V6 Mustangs
For Immediate Release
ATI is proud to announce the introduction of the first intercooled supercharger systems for 3.8 V6 Mustang applications. Intercooled ProCharger systems provide reliable 50-80% power gains on pump gas, with the coolest charge air temperatures and greatest engine reliability available. These systems are also the easiest to install, with no need to
relocate and recharge the air conditioning, modify the water pump, or punch a hole in the oil pan. These systems are 100% complete and can be bolted on in 6-8 hours with standard hand tools, and absolutely no fabrication or cutting of body panels. A three-year supercharger warranty is available with every V6 Mustang system.