From 3.8Wiki
Vortech
Vortech sells several kits for the V6 Mustang. Although none of them come with an intercooler, [1] now sells a intercooler upgrade kit that fits our V6's. Most splitport (1999-2004) V6's make right around 250rwhp with the stock pulley provided by Vortech.
Procharger
Procharger sells supercharger kits for 94-04 V6 Mustangs. You can get them with either 8psi or 11psi and with or without an intercooler. The 11psi intercooled kits put most splitport (1999-2004) V6's right around the 300rwhp mark.
Places to get a Procharger supercharger kit:
[2]
M90 Swap
This swap consists of the use of the 1989-1995 Thunderbird Supercoupe or The Cougar XR-7 supercharger top end and pulley system. This swap works on 1989-1998 single port 3.8L v6's as a direct fit with the use of the lower intake manifold. Some modificationwill need to be done to the brake lines and cooling system, besides that all the parts that are pulled from the SC setup bolt right on. You can expect 223rwhp and 300trq. from this setup.
M112
Mysteed Performance is currently producing a M112 supercharger kit for the 1999-2004 V6 Mustangs and those 1994-1998 V6 Mustangs that have done the splitport swap. Projected horsepower is between 260-290rwhp and 310-330rwtq at 7psi. The price for one of these kits is $2,800 plus shipping and the end user needs to supply a tune, boost gauge, and a 25% underdrive pulley and as of right now there is no intercooler upgrade for the M112's. PM Mysteed for more information on the kit or to purchase a kit.