4.6 running rich, randomly cutting out, idle randomly jumps and has no power above 3500 rpm

I bought a 1997 mustang with a 4.6 and a Vortech v1 supercharger, it only has 90,000 miles and has sat for a while. It ran ok when I got it, then the battery died and now it hasn’t been the same. I checked fuel pressure, 34-35 psi at idle unplugged vacuum and went to 40. I also checked the spark plug and gap 0.035. Replaced the alternator, fuel filter and and going to change the electric pump fuel management unit and fuel pressure regulator and I cleaned the Maf, air filter, iac. Sometimes it will run ok, other times it cuts out, bucks and revs on it own, it occasionally puffs black smoke on start up.
 
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@Vortechv1kylie That doesn't sound good! Does this have a standalone ECU. I'm not familiar with the older stangs. If it does; sounds like a good tune is needed. Have you checked the codes? Again sorry if you don't have an ECU then everything I'm saying is pointless. You had no issues until the battery died would lead me to believe a corrupted tune in the ECU. My mustang did this and I had to pay to have it re-tuned at a local shop.
 
I bought a 1997 mustang with a 4.6 and a Vortech v1 supercharger, it only has 90,000 miles and has sat for a while. It ran ok when I got it, then the battery died and now it hasn’t been the same. I checked fuel pressure, 34-35 psi at idle unplugged vacuum and went to 40. I also checked the spark plug and gap 0.035. Replaced the alternator, fuel filter and and going to change the electric pump fuel management unit and fuel pressure regulator and I cleaned the Maf, air filter, iac. Sometimes it will run ok, other times it cuts out, bucks and revs on it own, it occasionally puffs black smoke on start up.

Maybe it's running rich and you need a good tune for it. I agree with the guy above, It sounds like your tune may be off.