Dispite what others have said, do the split port swap, the heads and intakes are much better flowing over your single port (owned both a split and single port V6 and the split is far superior).
Now if you want to go FI, get the split port kit (I'd get a stage 2+ from SSM), then just get the needed parts from autozone or something to complete the swap (coil pack, wires, plugs, handful of other things).
Now when you're ready to do the S/C there's a couple of ways you can go, but one way growing in popularity with 99-04 sixers is putting on the M-112 supercharger from the 03/04 Cobra. SSM also sells the adaptor plate needed to put the M-112 on a sixer.
Now, IMO, there are much better S/Cs than the M-112. The M-112 is a roots blower, now it's one of the newest roots blowers, but still suffers the same problems as older models, they can get heat soaked (meaning loss of power after consistant boost), and they're not as effecient at making power as a twin screw or centrifugal. The advantage of a roots supercharger (and a twin screw which is a much more efficient supercharger, not sure if you can make a Kenne Bell or Whipple work on a V6, even with the bracket) over a centrifugal is that they make power very early on, and keep that power going, they don't need time to "boost" up. Downside is, they do tend to lag out a little bit after 3rd gear where as the centrifugals hold strong.
So at this point it's really up to you. personally, I'd do the stage 2+ split port swap, then in a year or two, do the M-112 eaton and do a pulley swap to get more boost. Vortech and Procharger are nice, but expensive (compared to the used M-112s), and are quite hard to find used for a sixer.
