Firstly your car doesn't have a distributer cap, it has a coil pack, similar in basic functionality but totally different.
If you're looking to do anything to the car you're looking at pretty much a complete restoration here. Keep in mind that car is now 20 years old and everything on it is likely....20 years old. The motor isn't totally gone yet, but it's definitely through half of it's life and it would not be a wise idea to mod such a motor.
If you're looking for power your best bet is going to also be your most expensive, and your lack of knowledge is going to hurt you a bit. So with that said your best route would be buying a completely new rebuilt engine block (you can usually get these for under $1000). Next, go to a junk yard or ebay (yuck) and find a set of 99-04 V6 heads and lower intake, have them cleaned and the heads machined and rebuilt and ported if you like. Then buy the M112 V6 kit (about $3000). Next buy a 99-04 V6 Wiring harness and ECU. Yes you can use most of your current harness on a 99-04 V6, however being 20 years old odds are spots of it are dry rotten and will fray/break upon touching them or removing sensors. Then buy 99-04 wires, coil, etc. Lastly buy your transmission of choice. If you get an auto make sure your get a 4R70W and the ECU to match. If you get a T5 or T45 manual again get the ecu to match. Me personally, since you're already deep in this thing, I'd get a T56 transmission. It'll work better with the supercharger and is much, much, much more durable than the T45/T5s which are a POS in my gods honest opinion for modded cars. Don't forget it would also be extremely wise to get a 8.8" rear end out of a GT/Cobra as your factory rear end would not be best for this setup.
Now with all this done you won't have a super fast street machine, at least not by modern terms, but if done correctly you will have a rebuilt car with all new components that offers decent modern performance. Yes, you will be able to have bought a newer/faster car with the money invested, but that's the price you pay for such investments. Also keep in mind none of this will really help the value of the car upon resell.
Serenity 08 Mustang GT - 295 RWHP, 315 TQ
Shelly 11 Mustang V6 - 270 RWHP, 260 TQ
95 Mustang 5.0 - N/A 250 RWHP, 275 TQ; S/C 400 RWHP, 400 TQ (sold)
99 Mustang SVT Cobra - 280 RWHP, 290 TQ (sold)
97 Mustang GT - 190 RWHP, 250 TQ (sold)
00 Mustang V6 - 145 RWHP, 184 TQ (sold)
98 Mustang V6 - 125 RWHP, 210 TQ (sold)